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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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2
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Nielsen M, Margaryan A, Nielsen TL, Enghoff H, Allentoft ME. Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Eastern Arc Mountains in Tanzania represent a hotspot for biological diversity of global importance. The level of endemism is high, and Eastern Arc biodiversity has been studied extensively in vertebrates and invertebrates, including millipedes. However, millipede evolution is vastly understudied at the molecular level. Therefore, we used next-generation ‘shotgun’ sequencing to obtain mitochondrial genome sequences of 26 museum specimens, representing six genera and 12 millipede species found across the Eastern Arc Mountains. Bayesian and maximum likelihood methods yielded consistent topologies with high node support, confirming a high level of congruence between molecular and morphological analyses. The only exception was a Tropostreptus sigmatospinus individual from Zanzibar, which was placed outside an otherwise monophyletic group consisting of mainland individuals of the same assumed species. For two species with a distribution across several mountain blocks (Tropostreptus sigmatospinus and Tropostreptus hamatus), each mountain population represents a distinct monophyletic lineage. In contrast, we also observe that distinct species exist sympatrically in the same montane forests, indicative of older speciation events that are not defined by current forest distribution. Our results are important for understanding speciation mechanisms in montane rain forests and highlight that ethanol-preserved invertebrates exhibit a tremendous potential for genomic analyses.
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Affiliation(s)
- Martin Nielsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
- Arctic Station, Faculty of Science, University of Copenhagen , Disko Island , Greenland
| | - Ashot Margaryan
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
| | - Tejs Lind Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
| | - Henrik Enghoff
- Natural History Museum of Denmark, University of Copenhagen , 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, WA , Australia
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3
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Abreu EF, Pavan SE, Tsuchiya MTN, McLean BS, Wilson DE, Percequillo AR, Maldonado JE. Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels. Mol Phylogenet Evol 2022; 175:107576. [PMID: 35809853 DOI: 10.1016/j.ympev.2022.107576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022]
Abstract
Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.
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Affiliation(s)
- Edson F Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
| | - Silvia E Pavan
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - Bryan S McLean
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Don E Wilson
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexandre R Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
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Salazar K, Nattier R. New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses. INSECTS 2020; 11:E766. [PMID: 33172182 PMCID: PMC7694756 DOI: 10.3390/insects11110766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 11/22/2022]
Abstract
Natural history collections house an important source of genetic data from yet unexplored biological diversity. Molecular data from museum specimens remain underexploited, which is mainly due to the degradation of DNA from specimens over time. However, Next-Generation Sequencing (NGS) technology can now be used to sequence "old" specimens. Indeed, many of these specimens are unique samples of nomenclatural types and can be crucial for resolving systematic or biogeographic scientific questions. Two ladybird beetle specimens from Patagonia corresponding to a new species of the genus Eriopis Mulsant were found in the collections of the Muséum national d'Histoire naturelle (MNHN), Paris. Here, we describe Eriopis patagonia Salazar, sp. nov. Total DNA of one of the two specimens was sequenced by NGS using a paired-end Illumina approach. We reconstruct and characterize the mitochondrial genome of this species (16,194 bp). Then, the protein-coding genes (PCGs) and ribosomal RNAs (rRNAs) were used to infer by maximum likelihood and Bayesian Inference the phylogenetic position of E. patagonia among 27 representatives of Coccinellidae. Phylogenetic analysis confirmed the position of Eriopis as sister group to Cycloneda Crotch. Hence, we highlight the high potential of sequencing technology for extracting molecular information from old specimens, which are used here for the systematic study of a genus, while demonstrating the importance of preserving biological collections.
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Affiliation(s)
- Karen Salazar
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
- Grupo de Investigación Insectos de Colombia, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá 111321, Colombia
| | - Romain Nattier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France;
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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6
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Declining genetic diversity of European honeybees along the twentieth century. Sci Rep 2020; 10:10520. [PMID: 32601293 PMCID: PMC7324561 DOI: 10.1038/s41598-020-67370-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
The European honeybee (Apis mellifera) is a key pollinator and has in the last decades suffered significant population decline. A combination of factors, including decrease in genetic diversity and introduction of Varroa mites, have been suggested to be responsible for these losses, but no definitive cause has yet been appointed. In Europe not only have wild colonies been severely affected, but managed hives have had a massive decline in numbers. To test the hypothesis that honeybees’ genetic diversity has decreased in the recent past, we used reduced representation genome sequencing of 40 historical honeybee specimens collected in Natural History collections across Europe and compared them to genomic data from 40 individuals from extant populations (collected post 2006). Our results are consistent with the existence of five evolutionary lineages as previously described, and show a decrease in genetic diversity between historical and extant individuals of the same lineage, as well as high levels of admixture in historical specimens. Our data confirm that a loss of genetic diversity has occurred during the last century, potentially increasing honeybees’ vulnerability to contemporary ecological and anthropogenic stressors.
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7
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Akankunda T, To H, Rodriguez Lopez C, Leijs R, Hogendoorn K. A method to generate multilocus barcodes of pinned insect specimens using MiSeq. Mol Ecol Resour 2020; 20. [PMID: 32104992 DOI: 10.1111/1755-0998.13143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/20/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023]
Abstract
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.
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Affiliation(s)
- Trace Akankunda
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Hien To
- The Bioinformatics Hub, The University of Adelaide, Adelaide, SA, Australia
| | - Carlos Rodriguez Lopez
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Remko Leijs
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,South Australian Museum, North Terrace, Adelaide, SA, Australia
| | - Katja Hogendoorn
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
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8
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Evaluation of DNA degradation and establishment of a degradation analysis model for Lepidoptera specimens. Biotechniques 2020; 68:138-147. [PMID: 31990210 DOI: 10.2144/btn-2019-0166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Millions of museum specimens are integral to biodiversity studies; however, DNA degradation may limit the ability to obtain DNA sequences. In this study, a degradation analysis model for Lepidoptera specimens was established. Based on this model, we revealed the characteristics of DNA fragment distribution caused by external DNA damage factors during specimen preservation. We found that the degree of DNA degradation increased over time; DNA degradation of spread and dried adult specimens was significantly higher than that in the folded and formalin-fixed larval specimens. However, the effects of folding wings on DNA degradation and the effects of the preservation method/stage (formalin-fixed larval vs air-dried adult specimens) were different for different species.
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9
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Ballare KM, Pope NS, Castilla AR, Cusser S, Metz RP, Jha S. Utilizing field collected insects for next generation sequencing: Effects of sampling, storage, and DNA extraction methods. Ecol Evol 2019; 9:13690-13705. [PMID: 31938475 PMCID: PMC6953651 DOI: 10.1002/ece3.5756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 08/20/2019] [Accepted: 09/15/2019] [Indexed: 01/04/2023] Open
Abstract
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we investigate the influence of five traditional insect capture and curation methods on Double-Digest Restriction Enzyme Associated DNA (ddRAD) sequencing success for three wild bee species. We sequenced a total of 105 specimens (between 7-13 specimens per species and treatment). We additionally investigated how different DNA quality metrics (including pre-sequence concentration and contamination) predicted downstream sequencing success, and also compared two DNA extraction methods. We report successful library preparation for all specimens, with all treatments and extraction methods producing enough highly reliable loci for population genetic analyses. Although results varied between species, we found that specimens collected by net sampling directly into 100% EtOH, or by passive trapping followed by 100% EtOH storage before pinning tended to produce higher quality ddRAD assemblies, likely as a result of rapid specimen desiccation. Surprisingly, we found that specimens preserved in propylene glycol during field sampling exhibited lower-quality assemblies. We provide recommendations for each treatment, extraction method, and DNA quality assessment, and further encourage researchers to consider utilizing a wider variety of specimens for genomic analyses.
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Affiliation(s)
- Kimberly M. Ballare
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCAUSA
| | - Nathaniel S. Pope
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of EntomologyPennsylvania State UniversityUniversity ParkPAUSA
| | - Antonio R. Castilla
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Centre for Applied Ecology “Prof. Baeta Neves”/INBIOInstitutoSuperior of AgronomyUniversity of LisbonLisbonPortugal
| | - Sarah Cusser
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - Richard P. Metz
- Genomics and Bioinformatics ServiceTexas A&M AgriLife ResearchCollege StationTXUSA
| | - Shalene Jha
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
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Trevisan B, Alcantara DM, Machado DJ, Marques FP, Lahr DJ. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 2019; 7:e7543. [PMID: 31565556 PMCID: PMC6746217 DOI: 10.7717/peerj.7543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel M.C. Alcantara
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Bioinformatics and Genomics / College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Fernando P.L. Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel J.G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
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11
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Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
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12
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Lalonde MML, Marcus JM. Entomological time travel: reconstructing the invasion history of the buckeye butterflies (genus Junonia) from Florida, USA. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01948-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Using host species traits to understand the Wolbachia infection distribution across terrestrial beetles. Sci Rep 2019; 9:847. [PMID: 30696916 PMCID: PMC6351630 DOI: 10.1038/s41598-018-38155-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022] Open
Abstract
Knowledge of Wolbachia prevalence with respect to its hosts is restricted mainly to taxonomic/phylogenetic context. In contrast, relations between infection and most host’s ecological and biological traits are poorly understood. This study aimed to elaborate on relations between bacteria and its beetle hosts in taxonomic and the ecological contexts. In particular, the goal is to verify which ecological and biological traits of beetles could cause them to be prone to be infected. Verification of Wolbachia infection status across 297 beetle taxa showed that approximately 27% of taxa are infected by supergroups A and B. Only minor support for coevolution between bacteria and its beetle hosts was observed in some genera of beetles, but in general coevolution between beetles and Wolbachia was rejected. Some traits of beetles were found to be unrelated to Wolbachia prevalence (type of range and thermal preferences); some traits were related with ambiguous effects (habitats, distribution, mobility and body size); some were substantially related (reproduction mode and trophy). The aforementioned summary does not show obvious patterns of Wolbachia prevalence and diversity in relation to host taxonomy, biology, and ecology. As both Wolbachia and Coleoptera are diverse groups, this lack of clear patterns is probably a reflection of nature, which is characterised by highly diversified and probably unstable relations.
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Kajtoch Ł, Kotásková N. Current state of knowledge on Wolbachia infection among Coleoptera: a systematic review. PeerJ 2018; 6:e4471. [PMID: 29568706 PMCID: PMC5846457 DOI: 10.7717/peerj.4471] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/17/2018] [Indexed: 11/20/2022] Open
Abstract
Background Despite great progress in studies on Wolbachia infection in insects, the knowledge about its relations with beetle species, populations and individuals, and the effects of bacteria on these hosts, is still unsatisfactory. In this review we summarize the current state of knowledge about Wolbachia occurrence and interactions with Coleopteran hosts. Methods An intensive search of the available literature resulted in the selection of 86 publications that describe the relevant details about Wolbachia presence among beetles. These publications were then examined with respect to the distribution and taxonomy of infected hosts and diversity of Wolbachia found in beetles. Sequences of Wolbachia genes (16S rDNA, ftsZ) were used for the phylogenetic analyses. Results The collected publications revealed that Wolbachia has been confirmed in 204 beetle species and that the estimated average prevalence of this bacteria across beetle species is 38.3% and varies greatly across families and genera (0–88% infected members) and is much lower (c. 13%) in geographic studies. The majority of the examined and infected beetles were from Europe and East Asia. The most intensively studied have been two groups of herbivorous beetles: Curculionidae and Chrysomelidae. Coleoptera harbor Wolbachia belonging to three supergroups: F found in only three species, and A and B found in similar numbers of beetles (including some doubly infected); however the latter two were most prevalent in different families. A total of 59% of species with precise data were found to be totally infected. Single infections were found in 69% of species and others were doubly- or multiply-infected. Wolbachia caused numerous effects on its beetle hosts, including selective sweep with host mtDNA (found in 3% of species), cytoplasmic incompatibility (detected in c. 6% of beetles) and other effects related to reproduction or development (like male-killing, possible parthenogenesis or haplodiploidy induction, and egg development). Phylogenetic reconstructions for Wolbachia genes rejected cospeciation between these bacteria and Coleoptera, with minor exceptions found in some Hydraenidae, Curculionidae and Chrysomelidae. In contrast, horizontal transmission of bacteria has been suspected or proven in numerous cases (e.g., among beetles sharing habitats and/or host plants). Discussion The present knowledge about Wolbachia infection across beetle species and populations is very uneven. Even the basic data about infection status in species and frequency of infected species across genera and families is very superficial, as only c. 0.15% of all beetle species have been tested so far. Future studies on Wolbachia diversity in Coleoptera should still be based on the Multi-locus Sequence Typing system, and next-generation sequencing technologies will be important for uncovering Wolbachia relations with host evolution and ecology, as well as with other, co-occurring endosymbiotic bacteria.
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Affiliation(s)
- Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences, Krakow, Poland
| | - Nela Kotásková
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Cotoras DD, Murray GGR, Kapp J, Gillespie RG, Griswold C, Simison WB, Green RE, Shapiro B. Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui. Genes (Basel) 2017; 8:genes8120403. [PMID: 29261166 PMCID: PMC5748721 DOI: 10.3390/genes8120403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/02/2017] [Accepted: 12/13/2017] [Indexed: 01/30/2023] Open
Abstract
Rapa Nui is one of the most remote islands in the world. As a young island, its biota is a consequence of both natural dispersals over the last ~1 million years and recent human introductions. It therefore provides an opportunity to study a unique community assemblage. Here, we extract DNA from museum-preserved and newly field-collected spiders from the genus Tetragnatha to explore their history on Rapa Nui. Using an optimized protocol to recover ancient DNA from museum-preserved spiders, we sequence and assemble partial mitochondrial genomes from nine Tetragnatha species, two of which were found on Rapa Nui, and estimate the evolutionary relationships between these and other Tetragnatha species. Our phylogeny shows that the two Rapa Nui species are not closely related. One, the possibly extinct, T. paschae, is nested within a circumtropical species complex (T. nitens), and the other (Tetragnatha sp. Rapa Nui) appears to be a recent human introduction. Our results highlight the power of ancient DNA approaches in identifying cryptic and rare species, which can contribute to our understanding of the global distribution of biodiversity in all taxonomic lineages.
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Affiliation(s)
- Darko D Cotoras
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
- Entomology Department, California Academy of Sciences, 55 Music Concourse Dr., Golden Gate Park, San Francisco, CA 94118, USA.
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Dr., Golden Gate Park, San Francisco, CA 94118, USA.
| | - Gemma G R Murray
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Rosemary G Gillespie
- Department of Environmental Science, University of California, 137 Mulford Hall, Berkeley, CA 94720-3114, USA.
| | - Charles Griswold
- Entomology Department, California Academy of Sciences, 55 Music Concourse Dr., Golden Gate Park, San Francisco, CA 94118, USA.
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Dr., Golden Gate Park, San Francisco, CA 94118, USA.
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One 2015; 10:e0143929. [PMID: 26716693 PMCID: PMC4696846 DOI: 10.1371/journal.pone.0143929] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/30/2023] Open
Abstract
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
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Timmermans MJTN, Viberg C, Martin G, Hopkins K, Vogler AP. Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12552] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martijn J. T. N. Timmermans
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
- Department of Natural Sciences; Middlesex University; Hendon Campus London NW4 4BT UK
| | - Carl Viberg
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Geoff Martin
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - Kevin Hopkins
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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Price BW, Henry CS, Hall AC, Mochizuki A, Duelli P, Brooks SJ. Singing from the grave: DNA from a 180 year old type specimen confirms the identity of Chrysoperla carnea (Stephens). PLoS One 2015; 10:e0121127. [PMID: 25853856 PMCID: PMC4390323 DOI: 10.1371/journal.pone.0121127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/11/2015] [Indexed: 11/28/2022] Open
Abstract
Historically serving as repositories for morphologically-based taxonomic research, natural history collections are now increasingly being targeted in studies utilizing DNA data. The development of advanced molecular techniques has facilitated extraction of useable DNA from old specimens, including type material. Sequencing diagnostic molecular markers from type material enables accurate species designation, especially where modern taxonomic hypotheses confirm morphologically cryptic species complexes. One such example is Chrysoperla carnea (Stephens), which belongs to a complex of about 20 cryptic species, most of which can only be reliably distinguished by their pre-mating courtship songs or by DNA analysis. The subtle morphological variation in the group has led to disagreement over the previous designation of the lectotype for C. carnea, an issue that has been further compounded because Chrysoperla carnea is a highly valued biological control agent in arable crops. Archival DNA extraction and sequencing from the 180 year old lectotype specimen, combined with Bayesian and Likelihood based phylogenetic analyses of modern specimens from the entire complex, were used to establish unambiguously the true identity of Chrysoperla carnea.
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Affiliation(s)
- Ben W. Price
- Life Sciences Department, Natural History Museum, London, England
| | - Charles S. Henry
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
| | - Andie C. Hall
- Core Research Laboratories, Natural History Museum, London, England
| | - Atsushi Mochizuki
- National Institute for Agro-Environmental Sciences, Tsukuba City, Ibaraki, Japan
| | - Peter Duelli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A 2014; 111:E5661-9. [PMID: 25512547 DOI: 10.1073/pnas.1416991111] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
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