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Liang K, Zhou L, Lei Q, Ruan T, Zhang M, Guo J, Brinker CJ, Zhu W. Deep silicification-assisted long-term preservation of structural and genomic information across biospecies: From micro to macro. Proc Natl Acad Sci U S A 2024; 121:e2408273121. [PMID: 39388268 DOI: 10.1073/pnas.2408273121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024] Open
Abstract
The concurrent preservation of morphological, structural, and genomic attributes within biological samples is paramount for comprehensive insights into biological phenomena and disease mechanisms. However, current preservation methodologies (e.g., cryopreservation, chemical reagent fixation, and bioplasticization) exhibit limitations in simultaneously achieving these critical combined goals. To address this gap, inspired by natural fossilization, here we propose "deep silicification," a room temperature technology that eliminates fixation requirements and overcomes the cold chain problem. By harnessing the synergy between ethanol and dimethyl sulfoxide, deep silicification significantly enhances silica penetration and accumulation within bioorganisms, thereby reinforcing structural integrity. This versatile and cost-effective approach demonstrates remarkable efficacy in preserving organismal morphology across various scales. Accelerated aging experiments underscore a 4,723-fold enhancement in genomic information storage over millennia, with whole-genome sequencing confirming nearly 100% fidelity. With its simplicity and reliability, "deep silicification" represents a paradigm shift in biological sample storage.
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Affiliation(s)
- Ke Liang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Liang Zhou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Qi Lei
- The Second Affiliated Hospital, Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou 510260, People's Republic of China
| | - Ting Ruan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Minmin Zhang
- Guangdong Provincial Key Laboratory of Nanophotonic Functional Materials and Devices, School of Optoelectronic Science and Engineering, South China Normal University, Guangzhou 510006, People's Republic of China
| | - Jimin Guo
- College of Materials Sciences and Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, NM 87131
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
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2
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Vander Pluym D, Mason NA. Toward a comparative framework for studies of altitudinal migration. Ecol Evol 2024; 14:e70240. [PMID: 39219567 PMCID: PMC11364985 DOI: 10.1002/ece3.70240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 08/07/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The study and importance of altitudinal migration has attracted increasing interest among zoologists. Altitudinal migrants are taxonomically widespread and move across altitudinal gradients as partial or complete migrants, subjecting them to a wide array of environments and ecological interactions. Here, we present a brief synthesis of recent developments in the field and suggest future directions toward a more taxonomically inclusive comparative framework for the study of altitudinal migration. Our framework centers on a working definition of altitudinal migration that hinges on its biological relevance, which is scale-dependent and related to fitness outcomes. We discuss linguistic nuances of altitudinal movements and provide concrete steps to compare altitudinal migration phenomena across traditionally disparate study systems. Together, our comparative framework outlines a "phenotypic space" that contextualizes the biotic and abiotic interactions encountered by altitudinal migrants from divergent lineages and biomes. We also summarize new opportunities, methods, and challenges for the ongoing study of altitudinal migration. A persistent, primary challenge is characterizing the taxonomic extent of altitudinal migration within and among species. Fortunately, a host of new methods have been developed to help researchers assess the taxonomic prevalence of altitudinal migration-each with their own advantages and disadvantages. An improved comparative framework will allow researchers that study disparate disciplines and taxonomic groups to better communicate and to test hypotheses regarding the evolutionary and ecological drivers underlying variation in altitudinal migration among populations and species.
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Affiliation(s)
- David Vander Pluym
- Department of Biological Sciences, Museum of Natural ScienceLouisiana State UniversityBaton RougeLouisianaUSA
| | - Nicholas A. Mason
- Department of Biological Sciences, Museum of Natural ScienceLouisiana State UniversityBaton RougeLouisianaUSA
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3
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Poulin R, Salloum PM, Bennett J. Evolution of parasites in the Anthropocene: new pressures, new adaptive directions. Biol Rev Camb Philos Soc 2024. [PMID: 38984760 DOI: 10.1111/brv.13118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Priscila M Salloum
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Jerusha Bennett
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, New Zealand
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4
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Liu X, Du W, Wang C, Wu Y, Chen W, Zheng Y, Wang M, Liu H, Yang Q, Qian S, Chen L, Liu C. A multilocus DNA mini-barcode assay to identify twenty vertebrate wildlife species. iScience 2023; 26:108275. [PMID: 38026223 PMCID: PMC10651681 DOI: 10.1016/j.isci.2023.108275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The world faces significant challenges in preserving the diversity of vertebrate species due to wildlife crimes. DNA barcoding, an effective molecular marker for insufficient nuclear DNA, is an authentic and quick identification technique to trace the origin of seized samples in forensic investigations. Here, we present a multiplex assay capable of identifying twenty vertebrate wildlife species utilizing twenty species-specific primers that target short fragments of the mitochondrial Cyt b, COI, 16S rRNA, and 12S rRNA genes. The assay achieved strong species specificity and sensitivity with a detection limit as low as 5 pg of DNA input. Additionally, it effectively discriminated a minor contributor (≥1%) from binary mixtures and successfully identified of noninvasive samples, inhibited DNA samples, artificially degraded DNA samples, and case samples, demonstrating a sensitive, robust, practical and easily interpretable tool in screening, and investigating forensic wildlife crimes.
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Affiliation(s)
- Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Weian Du
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong 528000, China
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yajiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yangyang Zheng
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Hong Liu
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Qianyong Yang
- College of Medicine of Jiujiang University, Jiujiang, Jiangxi 332000 China
| | - Shui Qian
- Foshan Public Security Bureau, Foshan, Guangdong 528000, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, Guangdong 510230, China
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5
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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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6
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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8
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Settlecowski AE, Marks BD, Manthey JD. Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens. Ecol Evol 2023; 13:e10407. [PMID: 37565027 PMCID: PMC10410627 DOI: 10.1002/ece3.10407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/28/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high-throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: (1) double-stranded DNA (dsDNA), single tube (KAPA); (2) single-stranded DNA (ssDNA), multi-tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi-tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best-performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.
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Affiliation(s)
- Amie E. Settlecowski
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Ben D. Marks
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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Pramasivan S, Low VL, Jeyaprakasam NK, Liew JWK, Ngui R, Vythilingam I. Cryptic Diversity and Demographic Expansion of Plasmodium knowlesi Malaria Vectors in Malaysia. Genes (Basel) 2023; 14:1369. [PMID: 37510274 PMCID: PMC10378955 DOI: 10.3390/genes14071369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although Malaysia is considered free of human malaria, there has been a growing number of Plasmodium knowlesi cases. This alarming trend highlighted the need for our understanding of this parasite and its associated vectors, especially considering the role of genetic diversity in the adaptation and evolution among vectors in endemic areas, which is currently a significant knowledge gap in their fundamental biology. Thus, this study aimed to investigate the genetic diversity of Anopheles balabacensis, Anopheles cracens, Anopheles introlatus, and Anopheles latens-the vectors for P. knowlesi malaria in Malaysia. Based on cytochrome c oxidase 1 (CO1) and internal transcribed spacer 2 (ITS2) markers, the genealogic networks of An. latens showed a separation of the haplotypes between Peninsular Malaysia and Malaysia Borneo, forming two distinct clusters. Additionally, the genetic distances between these clusters were high (2.3-5.2% for CO1) and (2.3-4.7% for ITS2), indicating the likely presence of two distinct species or cryptic species within An. latens. In contrast, no distinct clusters were observed in An. cracens, An. balabacensis, or An. introlatus, implying a lack of pronounced genetic differentiation among their populations. It is worth noting that there were varying levels of polymorphism observed across the different subpopulations, highlighting some levels of genetic variation within these mosquito species. Nevertheless, further analyses revealed that all four species have undergone demographic expansion, suggesting population growth and potential range expansion for these vectors in this region.
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Affiliation(s)
- Sandthya Pramasivan
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Van Lun Low
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Nantha Kumar Jeyaprakasam
- Biomedical Science Program, Center for Toxicology and Health Risk Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Jonathan Wee Kent Liew
- Environmental Health Institute, National Environment Agency, Singapore 569874, Singapore
| | - Romano Ngui
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak (UNIMAS), Kota Samarahan 94300, Sarawak, Malaysia
| | - Indra Vythilingam
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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Escobedo-Morales LA, Castañeda-Rico S, Mandujano S, León-Paniagua L, Maldonado JE. First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901. Mol Biol Rep 2023; 50:4851-4863. [PMID: 37039999 DOI: 10.1007/s11033-023-08407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.
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Affiliation(s)
- Luis A Escobedo-Morales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, Primer piso, Circuito de Posgrados, AP 70-153, Ciudad Universitaria, Mexico City, 04510, Mexico.
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA.
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
| | - Salvador Mandujano
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Xalapa, Veracruz, 91070, Mexico
| | - Livia León-Paniagua
- Museo de Zoología Alfonso L. Herrera, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
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11
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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12
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Haemosporidians in Non-Passerine Birds of Colombia: An Overview of the Last 20 Years of Research. DIVERSITY 2023. [DOI: 10.3390/d15010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Neotropics are highly diverse in avian species. Neotropical countries contribute a large part of the estimated diversity of haemosporidian parasites reported for the planet’s tropical zones. However, sampling is limited and biased, illustrated by only 30% of the genetic records (barcodes) from non-passerines, most of them not linked to a nominal species. This paper aimed to perform the molecular and morphological characterization of the haemosporidians that infect non-passerine birds from Colombia deposited in the biological collection named “Grupo de Estudio Relación Parásito Hospedero (GERPH)”. We analyzed 1239 samples from twelve biomes and two animal care facilities. Phylogenetic relationships using barcodes and mitochondrial genomes were estimated. In addition, the reports of haemosporidian infections in non-passerine birds from the Neotropics recorded after 1978 were summarized. We reported the presence of thirteen morphological haemosporidian species, four potential new species deposited in GERPH, a host range expansion for two Plasmodium species, and a barcode sequence for Haemoproteus caprimulgi. We confirmed the species associated with 56 molecular lineages reported in other neotropical countries at the genus level. Thus, biological collections and curated databases such as MalAvi are essential to support integrative approaches demanded in modern taxonomy.
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13
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Byerly PA, Chesser RT, Fleischer RC, McInerney N, Przelomska NAS, Leberg PL. Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic. Integr Comp Biol 2022; 62:1838-1848. [PMID: 35781565 DOI: 10.1093/icb/icac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023] Open
Abstract
Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.
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Affiliation(s)
- Paige A Byerly
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - R Terry Chesser
- Eastern Ecological Science Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708, USA.,National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA
| | - Robert C Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Nancy McInerney
- Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA
| | - Natalia A S Przelomska
- National Museum of Natural History, 10th St. and Constitution Avenue, NW, Washington, DC 20560, USA.,Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Avenue, NW, Washington, DC 20008, USA.,Royal Botanic Gardens, Kew, Richmond TW9 3AE, UK
| | - Paul L Leberg
- University of Louisiana at Lafayette, 104 E University Ave, Lafayette, LA 70504, USA
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14
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Brasil SNR, Kelemen EP, Rehan SM. Historic DNA uncovers genetic effects of climate change and landscape alteration in two wild bee species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01488-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Kessel GM, Alderslade P, Bilewitch JP, Schnabel KE, Gardner JPA. The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.
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Affiliation(s)
- Gustav M Kessel
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
| | - Philip Alderslade
- CSIRO Oceans and Atmosphere , Castray Esplanade, Hobart, TAS 7000 , Australia
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Kareen E Schnabel
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Jonathan P A Gardner
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
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16
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Dopheide A, Brav-Cubitt T, Podolyan A, Leschen RAB, Ward D, Buckley TR, Dhami MK. Fast-tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation. Mol Ecol Resour 2022. [PMID: 36345645 DOI: 10.1111/1755-0998.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
Despite recent advances in high-throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA-based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA database development, yet obtaining DNA barcodes from long-stored specimens may be difficult due to sample degradation. Here we demonstrate a sensitive and efficient laboratory and bioinformatic process for generating DNA barcodes from hundreds of invertebrate specimens simultaneously via the Illumina MiSeq system. Using this process, we recovered full-length (334) or partial (105) COI barcodes from 439 of 450 (98%) national collection-held invertebrate specimens. This included full-length barcodes from 146 specimens which produced low-yield DNA and no visible PCR bands, and which produced as little as a single sequence per specimen, demonstrating high sensitivity of the process. In many cases, the identity of the most abundant sequences per specimen were not the correct barcodes, necessitating the development of a taxonomy-informed process for identifying correct sequences among the sequencing output. The recovery of only partial barcodes for some taxa indicates a need to refine certain PCR primers. Nonetheless, our approach represents a highly sensitive, accurate and efficient method for targeted reference database generation, providing a foundation for DNA-based assessments and monitoring of biodiversity.
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Affiliation(s)
| | | | | | | | - Darren Ward
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R Buckley
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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17
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Lalueza-Fox C. Museomics. Curr Biol 2022; 32:R1214-R1215. [DOI: 10.1016/j.cub.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Human-induced evolution of salmon by means of unnatural selection. Proc Natl Acad Sci U S A 2022; 119:e2216526119. [PMID: 36279438 PMCID: PMC9636933 DOI: 10.1073/pnas.2216526119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Winchell KM, Aviles‐Rodriguez KJ, Carlen EJ, Miles LS, Charmantier A, De León LF, Gotanda KM, Rivkin LR, Szulkin M, Verrelli BC. Moving past the challenges and misconceptions in urban adaptation research. Ecol Evol 2022; 12:e9552. [PMID: 36425909 PMCID: PMC9679025 DOI: 10.1002/ece3.9552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 10/14/2023] Open
Abstract
Although the field of urban evolutionary ecology has recently expanded, much progress has been made in identifying adaptations that arise as a result of selective pressures within these unique environments. However, as studies within urban environments have rapidly increased, researchers have recognized that there are challenges and opportunities in characterizing urban adaptation. Some of these challenges are a consequence of increased direct and indirect human influence, which compounds long-recognized issues with research on adaptive evolution more generally. In this perspective, we discuss several common research challenges to urban adaptation related to (1) methodological approaches, (2) trait-environment relationships and the natural history of organisms, (3) agents and targets of selection, and (4) habitat heterogeneity. Ignoring these challenges may lead to misconceptions and further impede our ability to draw conclusions regarding evolutionary and ecological processes in urban environments. Our goal is to first shed light on the conceptual challenges of conducting urban adaptation research to help avoid the propagation of these misconceptions. We further summarize potential strategies to move forward productively to construct a more comprehensive picture of urban adaptation, and discuss how urban environments also offer unique opportunities and applications for adaptation research.
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Affiliation(s)
- Kristin M. Winchell
- Department of BiologyNew York UniversityNew YorkNYUSA
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Kevin J. Aviles‐Rodriguez
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusettsUSA
- Department of BiologyFordham UniversityBronxNew YorkUSA
| | - Elizabeth J. Carlen
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of BiologyFordham UniversityBronxNew YorkUSA
- Living Earth CollaborativeWashington University in St. LouisSt. LouisMissouriUSA
| | - Lindsay S. Miles
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et EvolutiveUniversité de Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - Luis F. De León
- Department of BiologyUniversity of Massachusetts BostonBostonMassachusettsUSA
| | - Kiyoko M. Gotanda
- Department of BiologyUniversité de SherbrookeSherbrookeQuebecCanada
- Department of Biological SciencesBrock UniversitySt. Catharine'sOntarioCanada
| | - L. Ruth Rivkin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of BiologyUniversity of Toronto MississaugaMississaugaOntarioCanada
- Centre for Urban EnvironmentsUniversity of Toronto MississaugaMississaugaOntarioCanada
| | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Brian C. Verrelli
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
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20
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Mitochondrial genes as strong molecular markers for species identification. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00393-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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21
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Halsey MK, Stuhler JD, Bayona-Vásquez NJ, Platt RN, Goetze JR, Martin RE, Matocha KG, Bradley RD, Stevens RD, Ray DA. Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size. PLoS One 2022; 17:e0274554. [PMID: 36099283 PMCID: PMC9469943 DOI: 10.1371/journal.pone.0274554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Species with low effective population sizes are at greater risk of extinction because of reduced genetic diversity. Such species are more vulnerable to chance events that decrease population sizes (e.g. demographic stochasticity). Dipodomys elator, (Texas kangaroo rat) is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread D. ordii (Ord’s kangaroo rat) is thought to exhibit relative geographic and demographic stability. We assessed the genetic variation of D. elator and D. ordii samples using 3RAD, a modified restriction site associated sequencing approach. We hypothesized that D. elator would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to D. ordii. We were also interested in identifying population structure within contemporary samples of D. elator and detecting genetic variation between temporal samples to understand demographic dynamics. We analyzed up to 61,000 single nucleotide polymorphisms. We found that genetic variability and effective population size in contemporary D. elator populations is lower than that of D. ordii. There is slight, if any, population structure within contemporary D. elator samples, and we found low genetic differentiation between spatial or temporal historical samples. This indicates little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of D. elator has remained stable despite reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract species extinction.
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Affiliation(s)
- Michaela K. Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - John D. Stuhler
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Roy N. Platt
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jim R. Goetze
- Natural Sciences Department, Laredo College, Laredo, Texas, United States of America
| | - Robert E. Martin
- Department of Biology, McMurry University, Abilene, Texas, United States of America
| | - Kenneth G. Matocha
- Department of Biology, South Arkansas Community College, El Dorado, Arkansas, United States of America
| | - Robert D. Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - Richard D. Stevens
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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22
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Pacheco C, Lobo D, Silva P, Álvares F, García EJ, Castro D, Layna JF, López-Bao JV, Godinho R. Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.970249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.
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23
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Salmona J, Dayon J, Lecompte E, Karamanlidis AA, Aguilar A, Fernandez de Larrinoa P, Pires R, Mo G, Panou A, Agnesi S, Borrell A, Danyer E, Öztürk B, Tonay AM, Anestis AK, González LM, Dendrinos P, Gaubert P. The antique genetic plight of the Mediterranean monk seal ( Monachus monachus). Proc Biol Sci 2022; 289:20220846. [PMID: 36043283 PMCID: PMC9428542 DOI: 10.1098/rspb.2022.0846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/30/2022] [Indexed: 12/14/2022] Open
Abstract
Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the world's most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate into four populations. This structure is probably the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (less than 500 km) and infrequent long-distance dispersal (less than 1500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.
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Affiliation(s)
- Jordi Salmona
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
| | - Julia Dayon
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
- CEFE, Université de Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Emilie Lecompte
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
| | - Alexandros A. Karamanlidis
- MOm/Hellenic Society for the Study and Protection of the Monk seal, Solomou Strasse 18, Athens 10682, Greece
| | - Alex Aguilar
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | | | - Rosa Pires
- Instituto das Florestas e Conservação da Natureza IP-RAM, Jardim Botânico da Madeira, Caminho do Meio, Bom Sucesso, Funchal, Madeira 9064-512, Portugal
| | - Giulia Mo
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Vitaliano Brancati 48, Rome 00144, Italy
| | - Aliki Panou
- Archipelagos - Environment and Development, Lourdata, Kefalonia 28100, Greece
| | - Sabrina Agnesi
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Vitaliano Brancati 48, Rome 00144, Italy
| | - Asunción Borrell
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Erdem Danyer
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
| | - Bayram Öztürk
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
- Faculty of Aquatic Sciences, Istanbul University, Kalenderhane Mah. Onaltı Mart Şehitleri Cad. No: 2 Fatih 34134 Istanbul, Turkey
| | - Arda M. Tonay
- Turkish Marine Research Foundation (TUDAV), PO Box 10, Beykoz, Istanbul, Turkey
- Faculty of Aquatic Sciences, Istanbul University, Kalenderhane Mah. Onaltı Mart Şehitleri Cad. No: 2 Fatih 34134 Istanbul, Turkey
| | | | - Luis M. González
- Subdirección General de Biodiversidad Terrestre y Marina, Ministerio para la Transición Ecológica y el Reto Demográfico, Pza. San Juan de la Cruz, 10, Madrid 28071, Spain
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk seal, Solomou Strasse 18, Athens 10682, Greece
| | - Philippe Gaubert
- Laboratoire Évolution et Diversité Biologique, IRD-CNRS-UPS, Université Paul Sabatier, 118 route de Narbonne, Toulouse 31062, France
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24
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Digging in a 120 years-old lunch: What can we learn from collection specimens of extinct species? PLoS One 2022; 17:e0270032. [PMID: 35793291 PMCID: PMC9258829 DOI: 10.1371/journal.pone.0270032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 06/02/2022] [Indexed: 12/03/2022] Open
Abstract
Studying collection specimens is often the only way to unravel information about recent extinctions. These can reveal knowledge on threats and life traits related to extinction, and contribute, by extrapolation, to the conservation of extant species. However, high-throughput sequencing methods have rarely been applied to extinct species to reveal information on their ecology. Insular species are especially prone to extinction. We studied the gut contents of three specimens of the extinct giant skink Chioninia coctei of the Cabo Verde Islands using microscopy and DNA-metabarcoding. The presence of Tachygonetria adult nematodes suggests plants as important diet items. Our metabarcoding approach also identified plants and, additionally, invertebrates, supporting the hypothesis of C. coctei’s generalist diet. The absence of vertebrates in the digestive contents may reflect the decline of seabirds on the Desertas Islands that could have contributed to the debilitation of the giant skink, already depleted by persecution and severe droughts. Even with a small sample size, this study contributes to shedding light on the trophic roles of this enigmatic extinct species and emphasizes the need to develop holistic conservation plans for island threatened taxa. Additionally, it illustrates the potential of integrating up-to-date molecular methods with traditional approaches to studying collection specimens to help to solve ecological puzzles in other ecosystems.
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25
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Salter JF, Hosner PA, Tsai WLE, McCormack JE, Braun EL, Kimball RT, Brumfield RT, Faircloth BC. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae). Mol Phylogenet Evol 2022; 175:107559. [PMID: 35803448 DOI: 10.1016/j.ympev.2022.107559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/22/2023]
Abstract
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.
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Affiliation(s)
- Jessie F Salter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
| | - Peter A Hosner
- Natural History Museum of Denmark, Center for Global Mountain Biodiversity, and Center for Macroecology, Evolution, and Climate, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Florida, Gainesville, FL, USA
| | - Whitney L E Tsai
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA
| | - John E McCormack
- Moore Laboratory of Biology, Occidental College, Los Angeles, CA, USA; Biology Department, Occidental College, Los Angeles, CA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Andreone F, Boero F, Bologna MA, Carpaneto GM, Castiglia R, Gippoliti S, Massa B, Minelli A. Reconnecting research and natural history museums in Italy and the need of a national collection biorepository. Zookeys 2022; 1104:55-68. [PMID: 36761931 PMCID: PMC9848790 DOI: 10.3897/zookeys.1104.79823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
In Italy, differently from other countries, a national museum of natural history is not present. This absence is due, among other reasons, to its historical political fragmentation up to 1870, which led to the establishment of medium-sized museums, mostly managed by local administrations or universities. Moreover, a change of paradigm in biological research, at the beginning of the 20th century, contributed to privilege experimental studies in universities and facilitated the dismissal of descriptive and exploratory biology, which formed the basis of the taxonomic research carried out by natural history museums. Consequently, only a few museums have a provision of curatorial staff, space and material resources adequate to maintain their original mission of discovering the natural world, by conducting a regular research activity accompanied by field campaigns. The creation of a national research centre for the study of biodiversity, facilitating interconnections among the existing natural history museums could be a solution and is here supported, together with a centralised biorepository to host collections and vouchers, to the benefit of current and future taxonomic research and environmental conservation. Such an institution should find place and realisation within the recently proposed National Biodiversity Future Center (NBFC) planned within the National Plan of Recovery and Resilience (PNRR). Pending upon the creation of this new national centre, a network among the existing museums should coordinate their activities.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123 Torino, ItalyMuseo Regionale di Scienze NaturaliTorinoItaly
| | - Ferdinando Boero
- Università di Napoli Federico II, CNR-IAS, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, ItalyUniversità di Napoli Federico IINapoliItaly
| | - Marco A. Bologna
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Giuseppe M. Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università “La Sapienza” di Roma, Via A. Borelli, 50, I-00161 Roma, ItalyUniversità “La Sapienza” di RomaRomaItaly
| | - Spartaco Gippoliti
- Società Italiana per la Storia della Fauna “Giuseppe Altobello”, Viale Liegi, 48A, I-00198 Roma, ItalySocietà Italiana per la Storia della Fauna “Giuseppe Altobello”RomeItaly
| | - Bruno Massa
- Dipartimento di Scienze agrarie, alimentari e forestali, Università di Palermo, Viale Scienze, 13, I-90128 Palermo, ItalyUniversità di PalermoPalermoItaly
| | - Alessandro Minelli
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi, 58B, I-35131 Padova, ItalyUniversità di PadovaPadovaItaly
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27
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Hohwieler KR, Villiers DL, Cristescu RH, Frere CH. Genetic erosion detected in a specialist mammal living in a fast‐developing environment. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katrin R. Hohwieler
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | | | - Romane H. Cristescu
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | - Celine H. Frere
- School of Biological Sciences University of Queensland St Lucia QLD Australia
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28
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Irestedt M, Thörn F, Müller IA, Jønsson KA, Ericson PGP, Blom MPK. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins. Mol Ecol Resour 2022; 22:2672-2684. [PMID: 35661418 PMCID: PMC9542604 DOI: 10.1111/1755-0998.13660] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
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Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Filip Thörn
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Ingo A Müller
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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29
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González AD, Lotta-Arevalo I, Fuentes-Rodríguez GA, Macías-Zacipa J, Acevedo-Cendales LD, Matta NE. Is Haemoproteus gabaldoni a valid species? An approach from morphology and molecular tools applied to parasites of Anseriformes. Acta Trop 2022; 233:106540. [PMID: 35623401 DOI: 10.1016/j.actatropica.2022.106540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022]
Abstract
Currently, there are three recognized species of haemoproteids infecting Anseriformes: Haemoproteus nettionis, H. macrovacuolatus, and H. greineri. Unfortunately, genetic information associated with a morphotype is available only for H. macrovacuolatus. We recently found a parasite morphologically compatible with Haemoproteus gabaldoni, a species Bennet (1993) described in a Cairina moschata (Muscovy duck) from Venezuela. This species was synonymized to H. nettionis by Valkiūnas (2005), arguing not enough morphological differentiation between them; it was said that H. greineri could be as well a synonym of H. nettionis. In this study, we aimed to provide evidence to determine if Haemoproteus gabaldoni is a different species of H. nettionis and help to clarify other species status. We first performed morphological and morphometrical analyses and compared this information against the parahapantotypes of H. greineri, H. gabaldoni and material diagnosed as H. nettionis provided by the International Reference center for Avian Haematozoa (IRCAH), and H. macrovacuolatus from the Host-Parasite Relationship Study Group (GERPH, in Spanish Grupo de Estudio Relación Parásito Hospedero) biological collection. We used Principal Component Analysis (PCA) of dimensionless standard morphometrical variables from gametocytes. Furthermore, we amplified a small fragment of cytochrome b (cyt b) to compare the sequence with information in GenBank and Malavi through phylogenetic analyses and haplotype networks. PCA analyses revealed the presence of three distinct groups in the samples studied, supported in the morphological traits of each parasite species analyzed; phylogenetic analyses grouped parasite lineages separately according to the host and continent of provenance. Such results indicate that, H. gabaldoni, is a different species from H. nettionis. One more time, it is demonstrated the importance of linking barcode surveys to morphological studies. Finally, it is highlighted the importance of biological collections as repositories of worldwide biodiversity.
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Affiliation(s)
- Angie D González
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia.
| | - Ingrid Lotta-Arevalo
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
| | - Gustavo A Fuentes-Rodríguez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia; Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Sede, Bogotá, Colombia
| | - Jhon Macías-Zacipa
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia; Programa Bacteriología y Laboratorio Clínico, Facultad de Ciencias de la Salud, Universidad Colegio Mayor de Cundinamarca, Bogotá, Colombia
| | | | - Nubia E Matta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
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30
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Porretta D, Mastrantonio V, Lucchesi V, Bellini R, Vontas J, Urbanelli S. Historical samples reveal a combined role of agriculture and public-health applications in vector resistance to insecticides. PEST MANAGEMENT SCIENCE 2022; 78:1567-1572. [PMID: 34984788 PMCID: PMC9303699 DOI: 10.1002/ps.6775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Insecticide resistance is the major threat to vector control and for the prevention of vector-borne diseases. Because almost all insecticides used against insect vectors are or have been used in agriculture, a connection between agricultural insecticide use and resistance in insect vectors has been hypothesized. However, it is challenging to find a causal link between past agricultural use of insecticides and current resistance in vector populations without historical data series. Here we investigated the relative contribution across time of agricultural and public-health insecticide applications in selecting for diflubenzuron (DFB) resistance in Culex pipiens populations. Using DNA sequencing, we looked for DFB resistant mutations in current and historical mosquito samples, dating back to the 1980s-1990s, when DFB was used in agriculture but not yet in mosquito control. RESULTS In the samples collected before the introduction of DFB in vector control, we found the resistant mutation I1043M in rural regions but not any of the neighboring urban and natural areas, indicating that the selection pressure was derived by agriculture. However, after the introduction of DFB for vector control, the resistant mutations were found across all study areas showing that the initial selection from agriculture was further boosted by the selection pressure imposed by the mosquito control applications in the 2000s. CONCLUSIONS Our findings support a combined role of agricultural and public-health use of insecticides in vector resistance across time and call for specific actions in integrated resistance management, including increased communication between agriculture and health practitioners. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | | | | | - Romeo Bellini
- Medical and Veterinary Entomology DepartmentCentro Agricoltura Ambiente ‘G. Nicoli’BolognaItaly
| | - John Vontas
- Department of Crop Science, Pesticide Science LabAgricultural University of AthensAthensGreece
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology HellasHeraklion, CreteGreece
| | - Sandra Urbanelli
- Department of Environmental BiologySapienza University of RomeRomeItaly
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31
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Kearns AM, Campana MG, Slikas B, Berry L, Saitoh T, Cibois A, Fleischer RC. Conservation genomics and systematics of a near-extinct island radiation. Mol Ecol 2022; 31:1995-2012. [PMID: 35119154 DOI: 10.1111/mec.16382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mtDNA, nuclear SNPs support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographic structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that predate modern anthropogenic threats require further study with denser population sampling. Our study highlights the value conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragments their ranges and contributes to rapid declines in population abundances.
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Affiliation(s)
- Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Beth Slikas
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA.,Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Lainie Berry
- Department of Lands and Natural Resources, Commonwealth of the Northern Mariana Islands, Saipan, MP, 96950, USA.,Hawaii Department of Land and Natural Resources-Division of Forestry and Wildlife, Honolulu, HI, 96813, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
| | - Alice Cibois
- Natural History Museum of Geneva, CP, 6434, 1211, Geneva, Switzerland
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoological Park and Conservation Biology Institute, Washington, DC, 20008, USA
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32
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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern. Heredity (Edinb) 2022; 128:159-168. [PMID: 35082388 PMCID: PMC8897408 DOI: 10.1038/s41437-022-00499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Abstract
A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.
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Willi Y, Kristensen TN, Sgrò CM, Weeks AR, Ørsted M, Hoffmann AA. Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species. Proc Natl Acad Sci U S A 2022; 119:e2105076119. [PMID: 34930821 PMCID: PMC8740573 DOI: 10.1073/pnas.2105076119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Torsten N Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew R Weeks
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
- Cesar Australia, Brunswick, VIC 3056, Australia
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
- Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia;
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34
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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35
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DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-10626. [PMID: 35716293 PMCID: PMC9206398 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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Yamashita Y, Ogura‐Tsujita Y, Nagata N, Kurosawa T, Yukawa T. Molecular identification of seed‐feeding flies dissected from herbarium specimens clarifies the 100‐year history of parasitism by
Japanagromyza tokunagai
in Japan. Ecol Res 2021. [DOI: 10.1111/1440-1703.12283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yumi Yamashita
- Graduate School of Symbiotic Systems Science and Technology Fukushima University 1 Kanayagawa, Fukushima Fukushima Japan
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Yuki Ogura‐Tsujita
- Faculty of Agriculture Saga University, 1 Honjyo Saga Japan
- United Graduate School of Agricultural Sciences Kagoshima University Kagoshima Japan
| | - Nobuaki Nagata
- Department of Anthropology National Museum of Nature and Science Tsukuba, Ibaraki Japan
| | - Takahide Kurosawa
- Faculty of Symbiotic Systems Science Fukushima University Fukushima Fukushima Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden National Museum of Nature and Science Tsukuba, Ibaraki Japan
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37
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The history of genetic diversity and effective population size of an isolated Microtus oeconomus population on Kis Balaton. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00199-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Setzke C, Wong C, Russello MA. Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon. Sci Rep 2021; 11:22798. [PMID: 34815428 PMCID: PMC8611073 DOI: 10.1038/s41598-021-01958-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population history and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism genotypic data from archival scale samples, and applied this approach to a study of kokanee salmon (Oncorhynchus nerka) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (> 90% average genotyping across all individuals) and low genotyping error (< 0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrated GT-seq as a valuable tool for collecting genome-wide data from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.
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Affiliation(s)
- Christopher Setzke
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Carmen Wong
- Parks Canada Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada.
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Spatial and temporal patterns of genetic diversity in Bombus terrestris populations of the Iberian Peninsula and their conservation implications. Sci Rep 2021; 11:22471. [PMID: 34795335 PMCID: PMC8602315 DOI: 10.1038/s41598-021-01778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022] Open
Abstract
The bumblebee Bombus terrestris is used worldwide for crop pollination. Despite its positive impact on crop yield, it has become a widespread threat to biodiversity due to its interactions with local bumblebee populations. Commercial subspecies introduced to the Iberian Peninsula since the 1990s without any regulation have colonized the environment, with evidence of naturalization and introgression with the endemic subspecies Bombus terrestris lusitanicus. We have used mitochondrial and nuclear genetic data to describe the current genetic diversity of the Iberian population and to estimate the expansion of commercial bumblebees. Samples from the natural distribution range of the commercial subspecies, the natural intergradation area between the two subspecies and from a period prior to the use of commercial colonies (i.e., before the 1990s) have been used for comparison. Our results show that the mitochondrial haplotype of the commercial breeds has spread throughout the territory, which, together with subtle changes observed in the nuclear genetic diversity of the populations, indicates that hybridization and consequent introgression are occurring in most of the peninsula. It is, therefore, necessary to improve the existing legislation concerning the management and exportation of commercial bumblebees to conserve locally adapted populations.
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40
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Salado I, Fernández-Gil A, Vilà C, Leonard JA. Automated genotyping of microsatellite loci from feces with high throughput sequences. PLoS One 2021; 16:e0258906. [PMID: 34695152 PMCID: PMC8544849 DOI: 10.1371/journal.pone.0258906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.
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Affiliation(s)
- Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
| | - Alberto Fernández-Gil
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
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41
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Swope SM, Soto TY, Rahman-Khan Arana N. Historic DNA reveals genetic consequences of fragmentation in an endangered, endemic mustard. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01406-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Lampert S, Ingle RA, Jackson JA, Gopal K, Plön S. Low mitochondrial genetic diversity in the Indian Ocean humpback dolphin Sousa plumbea in South African waters. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Indian Ocean humpback dolphin Sousa plumbea has been described as South Africa’s most endangered marine mammal due to its low abundance, reliance on coastal habitats with increasing anthropogenic threats and high rates of mortality from bycatch in bather protection nets (BPNs). Although the species has been well studied in South Africa, only a single study has examined its molecular ecology to date, and its population structure remains poorly understood. However, understanding population structure is vital for the conservation and management of a species. To address these research gaps for S. plumbea in South African waters, we analysed the mitochondrial D-loop of 157 museum skin and tooth samples collected between 1963 and 2017 from across the species’ geographic range in South Africa. Our data show that the humpback dolphin has extremely low mitochondrial diversity (haplotype diversity, HD = 0.47; nucleotide diversity, π = 0.2%) with only 3 haplotypes identified, which is comparable to the Critically Endangered Māui dolphin Cephalorhynchus hectori maui and the Critically Endangered Mekong population of Irrawaddy dolphin Orcaella brevirostris. Mitochondrial genetic diversity has not changed significantly in the last 50 yr, despite the high levels of bycatch in BPNs over this time period. Furthermore, we found no evidence of differentiation between dolphins from the KwaZulu-Natal Coast and the Cape South Coast (Western Cape and Eastern Cape). The extremely low mitochondrial diversity we found adds to the growing body of evidence that the humpback dolphin is becoming increasingly vulnerable and that urgent conservation efforts are required for the survival of the species.
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Affiliation(s)
- S Lampert
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7700, South Africa
| | - RA Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7700, South Africa
| | - JA Jackson
- British Antarctic Survey, Cambridge CB3 0ET, UK
| | - K Gopal
- Natural Science Collections Facility (South African National Biodiversity Institute), Pretoria 0186, South Africa
- Department of Natural History, Iziko South African Museums, Cape Town 8001, South Africa
| | - S Plön
- Bayworld Centre for Research and Education (BCRE), Port Elizabeth 6013, South Africa
- Division of Medical Virology, Department of Pathology, Stellenbosch University, Cape Town 7505, South Africa
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43
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Mining museums for historical DNA: advances and challenges in museomics. Trends Ecol Evol 2021; 36:1049-1060. [PMID: 34456066 DOI: 10.1016/j.tree.2021.07.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/22/2023]
Abstract
Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
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44
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Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS One 2021; 16:e0256353. [PMID: 34424926 PMCID: PMC8382189 DOI: 10.1371/journal.pone.0256353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.
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Affiliation(s)
- Claus M. Zacho
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martina A. Bager
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Arne R. Rasmussen
- Institute of Conservation, Royal Danish Academy—Architecture, Design, Conservation, Copenhagen, Denmark
| | - Morten E. Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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45
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Abstract
The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.
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46
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O'Connell KA, Mulder KP, Wynn A, de Queiroz K, Bell RC. Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets. Mol Ecol Resour 2021; 22:487-502. [PMID: 34329532 DOI: 10.1111/1755-0998.13481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/10/2021] [Accepted: 07/14/2021] [Indexed: 12/17/2022]
Abstract
Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.
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Affiliation(s)
- Kyle A O'Connell
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA.,Biomedical Data Science Lab, Deloitte Consulting LLP, Arlington, Virginia, USA
| | - Kevin P Mulder
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Department of Herpetology, California Academy of Sciences, San Francisco, California, USA
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47
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Rodrigues MF, Cogni R. Genomic Responses to Climate Change: Making the Most of the Drosophila Model. Front Genet 2021; 12:676218. [PMID: 34326859 PMCID: PMC8314211 DOI: 10.3389/fgene.2021.676218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
It is pressing to understand how animal populations evolve in response to climate change. We argue that new sequencing technologies and the use of historical samples are opening unprecedented opportunities to investigate genome-wide responses to changing environments. However, there are important challenges in interpreting the emerging findings. First, it is essential to differentiate genetic adaptation from phenotypic plasticity. Second, it is extremely difficult to map genotype, phenotype, and fitness. Third, neutral demographic processes and natural selection affect genetic variation in similar ways. We argue that Drosophila melanogaster, a classical model organism with decades of climate adaptation research, is uniquely suited to overcome most of these challenges. In the near future, long-term time series genome-wide datasets of D. melanogaster natural populations will provide exciting opportunities to study adaptation to recent climate change and will lay the groundwork for related research in non-model systems.
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Affiliation(s)
- Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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48
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Filonzi L, Vaghi M, Ardenghi A, Rontani PM, Voccia A, Nonnis Marzano F. Efficiency of DNA Mini-Barcoding to Assess Mislabeling in Commercial Fish Products in Italy: An Overview of the Last Decade. Foods 2021; 10:foods10071449. [PMID: 34206502 PMCID: PMC8305242 DOI: 10.3390/foods10071449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 11/24/2022] Open
Abstract
The problem of fish traceability in processed products is still an important issue in food safety. Major attention is nowadays dedicated to consumer health and prevention of possible frauds regulated by national and international laws. For this reason, a technical approach is fundamental in revealing mislabeling at different levels. In particular, the use of genetic markers has been standardized and DNA barcoding is considered the gold-standard strategy to examine and prevent species substitution. Considering the richness of available DNA databases, it is nowadays possible to rapidly reach a reliable taxonomy at the species level. Among different approaches, an innovative method based on DNA mini barcoding has recently been proposed at an international level. Starting from this evidence, we herein illustrate an investigation dealing with the evolution of this topic in Italy over the last decade. The molecular analysis of 71 commercial fish samples based on mini-COI sequencing with two different primer sets reached an amplification success rate of 87.3 and 97.2%. The investigation revealed four major frauds (5.8%) and four minor ones (5.8%). Results highlighted a decrease in incorrect labeling in Italy from 32% to 11.6% over the last decade, although a recurrent involvement of “endangered” species sensu IUCN was still observed.
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49
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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50
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Ewers-Saucedo C, Allspach A, Barilaro C, Bick A, Brandt A, Fiege D, Füting S, Hausdorf B, Hayer S, Husemann M, Joger U, Kamcke C, Küster M, Lohrmann V, Martin I, Michalik P, Reinicke GB, Schwentner M, Stiller M, Brandis D. Natural history collections recapitulate 200 years of faunal change. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201983. [PMID: 33996123 PMCID: PMC8059531 DOI: 10.1098/rsos.201983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Changing species assemblages represent major challenges to ecosystems around the world. Retracing these changes is limited by our knowledge of past biodiversity. Natural history collections represent archives of biodiversity and are therefore an unparalleled source to study biodiversity changes. In the present study, we tested the value of natural history collections for reconstructing changes in the abundance and presence of species over time. In total, we scrutinized 17 080 quality-checked records for 242 epibenthic invertebrate species from the North and Baltic Seas collected throughout the last 200 years. Our approaches identified eight previously reported species introductions, 10 range expansions, six of which are new to science, as well as the long-term decline of 51 marine invertebrate species. The cross-validation of our results with published accounts of endangered species and neozoa of the area confirmed the results for two of the approaches for 49 to 55% of the identified species, and contradicted our results for 9 to 10%. The results based on relative record trends were less validated. We conclude that, with the proper approaches, natural history collections are an unmatched resource for recovering early species introductions and declines.
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Affiliation(s)
- Christine Ewers-Saucedo
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Andreas Allspach
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Christina Barilaro
- Landesmuseum Natur und Mensch Oldenburg, Damm 38-44, 26135 Oldenburg, Germany
| | - Andreas Bick
- Zoological Collections of the University of Rostock, Institute for Biological Sciences, General and Systematic Zoology, Universitätsplatz 2, 18055 Rostock, Germany
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe-University of Frankfurt, FB 15, Institute for Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - Dieter Fiege
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Susanne Füting
- Museum für Natur und Umwelt Lübeck, Musterbahn 8, 23552 Lübeck, Germany
| | - Bernhard Hausdorf
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Sarah Hayer
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Martin Husemann
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Claudia Kamcke
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Mathias Küster
- Müritzeum, Zur Steinmole 1, 17192 Waren (Müritz), Germany
| | - Volker Lohrmann
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Ines Martin
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Peter Michalik
- Zoologisches Museum der Universität Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | | | - Martin Schwentner
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
- Naturhistorisches Museum Wien, Burgring 7, 1140 Wien, Austria
| | - Michael Stiller
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Dirk Brandis
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
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