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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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3
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Redihough J, Russo IRM, Stewart AJA, Malenovský I, Stockdale JE, Moorhouse-Gann RJ, Wilson MR, Symondson WOC. Species Separation within, and Preliminary Phylogeny for, the Leafhopper Genus Anoscopus with Particular Reference to the Putative British Endemic Anoscopus duffieldi (Hemiptera: Cicadellidae). INSECTS 2020; 11:E799. [PMID: 33202804 PMCID: PMC7697789 DOI: 10.3390/insects11110799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/11/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
The subfamily Aphrodinae (Hemiptera: Cicadellidae) contains ~33 species in Europe within four genera. Species in two genera in particular, Aphrodes and Anoscopus, have proved to be difficult to distinguish morphologically. Our aim was to determine the status of the putative species Anoscopus duffieldi, found only on the RSPB Nature Reserve at Dungeness, Kent, a possible rare UK endemic. DNA from samples of all seven UK Anoscopus species (plus Anoscopusalpinus from the Czech Republic) were sequenced using parts of the mitochondrial cytochrome oxidase I and 16S rRNA genes. Bayesian inference phylogenies were created. Specimens of each species clustered into monophyletic groups, except for Anoscopusalbifrons, A. duffieldi and Anoscopuslimicola. Two A. albifrons specimens grouped with A. duffieldi repeatedly with strong support, and the remaining A. albifrons clustered within A. limicola. Genetic distances suggest that A. albifrons and A. limicola are a single interbreeding population (0% divergence), while A. albifrons and A. duffieldi diverged by only 0.28%. Shared haplotypes between A. albifrons, A. limicola and A. duffieldi strongly suggest interbreeding, although misidentification may also explain these topologies. However, all A. duffieldi clustered together in the trees. A conservative approach might be to treat A. duffieldi, until other evidence is forthcoming, as a possible endemic subspecies.
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Affiliation(s)
- Joanna Redihough
- Cardiff School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (J.R.); (I.-R.M.R.); (J.E.S.); (R.J.M.-G.)
| | - Isa-Rita M. Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (J.R.); (I.-R.M.R.); (J.E.S.); (R.J.M.-G.)
| | - Alan J. A. Stewart
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, East Sussex, UK;
| | - Igor Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, CZ-611 37 Brno, Czech Republic;
| | - Jennifer E. Stockdale
- Cardiff School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (J.R.); (I.-R.M.R.); (J.E.S.); (R.J.M.-G.)
| | - Rosemary J. Moorhouse-Gann
- Cardiff School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (J.R.); (I.-R.M.R.); (J.E.S.); (R.J.M.-G.)
| | - Michael R. Wilson
- Department of Natural Sciences, National Museum of Wales, Cardiff CF10 3NP, UK;
| | - William O. C. Symondson
- Cardiff School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK; (J.R.); (I.-R.M.R.); (J.E.S.); (R.J.M.-G.)
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Bell RC, Mulcahy DG, Gotte SW, Maley AJ, Mendoza C, Steffensen G, Barron II JC, Hyman O, Flint W, Wynn A, Mcdiarmid RW, Mcleod DS. The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Steve W. Gotte
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - Abigail J. Maley
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
- Division of Integrated Sciences, Wilson College, Chambersburg, PA 17201, USA
| | - Cerrie Mendoza
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
| | - Gregory Steffensen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Joseph C. Barron II
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| | - Oliver Hyman
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - William Flint
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roy W. Mcdiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - David S. Mcleod
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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Trichas A, Smirli M, Papadopoulou A, Anastasiou I, Keskin B, Poulakakis N. Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Abstract
The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.
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Affiliation(s)
- Apostolos Trichas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
| | - Maria Smirli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioannis Anastasiou
- Section of Zoology – Marine Biology, Department of Biology, University of Athens, Panepistimioupoli, GR-157 84 Athens, Greece
| | - Bekir Keskin
- Zoology Department, Section of Biology, Faculty of Science, Ege University, Bornova-Izmir, Turkey
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio, Greece
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Lonsinger RC, Daniel D, Adams JR, Waits LP. Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections. J Mammal 2019. [DOI: 10.1093/jmammal/gyz112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractSpecimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.
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Affiliation(s)
- Robert C Lonsinger
- Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - David Daniel
- Economics, Applied Statistics and International Business Department, New Mexico State University, Las Cruces, NM, USA
| | - Jennifer R Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
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Antoniou A, Frantzis A, Alexiadou P, Paschou N, Poulakakis N. Evidence of introgressive hybridization between Stenella coeruleoalba and Delphinus delphis in the Greek Seas. Mol Phylogenet Evol 2018; 129:325-337. [PMID: 30218775 DOI: 10.1016/j.ympev.2018.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 05/29/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
Natural interspecific hybridization might be more important for the evolutionary history and speciation of animals than previously thought, considering several demographic and life history traits as well as habitat disturbance as factors that promote it. In this aspect, cetaceans comprise an interesting case in which the occurrence of sympatric species in mixed associations provides excellent opportunities for interspecific sexual interaction and the potential for hybridization. Here, we present evidence of natural hybridization for two cetacean species commonly occurring in the Greek Seas (Stenella coeruleoalba and Delphinus delphis), which naturally overlap in the Gulf of Corinth by analyzing highly resolving microsatellite DNA markers and mitochondrial DNA sequences in skin samples from 45 individuals of S. coeruleoalba, 12 D. delphis and three intermediate morphs. Employing several phylogenetic and population genetic approaches, we found 15 individuals that are potential hybrids including the three intermediate morphs, verifying the occurrence of natural hybridization between species of different genera. Their hybrids are fertile and able to reproduce not only with the other hybrids but also with each of the two-parental species. However, current evidence does not allow firm conclusions whether hybridization might constitute a step towards the generation of a new species and/or the swan song of an already existing species (i.e., D. delphis). Given that the focal species form mixed pods in several areas of Mediterranean, this study is an excellent opportunity to understand the mechanisms leading to hybridization in the context of gene flow and urges for the evaluation of the genetic status of common dolphins in the Mediterranean.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Irakleio, Crete, Greece.
| | - Alexandros Frantzis
- Pelagos Cetacean Research Institute, Terpsichoris 21, 16671 Vouliagmeni, Greece
| | - Paraskevi Alexiadou
- Pelagos Cetacean Research Institute, Terpsichoris 21, 16671 Vouliagmeni, Greece
| | - Nefeli Paschou
- Department of Biology, School of Sciences and Engineering, University of Crete, Vasilika Vouton, Gr-71300 Heraklion, Crete, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av., GR-71409 Heraklion, Crete, Greece
| | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Vasilika Vouton, Gr-71300 Heraklion, Crete, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av., GR-71409 Heraklion, Crete, Greece
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8
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Sarot E, Carillo-Baraglioli MF, Duranthon F, Péquignot A, Pyronnet S. Assessment of alternatives to environmental toxic formalin for DNA conservation in biological specimens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16985-16993. [PMID: 28580543 DOI: 10.1007/s11356-017-9349-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
One essential step of museum and clinical specimen preservation is immersion in a fixative fluid to prevent degradation. Formalin is the most largely used fixative, but its benefit is balanced with its toxic and carcinogenic status. Moreover, because formalin-fixation impairs nucleic acids recovery and quality, current museum wet collections and formalin-fixed, paraffin-embedded clinical samples do not represent optimal tanks of molecular information. Our study has been developed to compare formalin to two alternative fixatives (RCL2® and ethanol) in a context of molecular exploitation. Based on a unique protocol, we created mammalian fixed collections, simulated the impact of time on preservation using an artificial ageing treatment and followed the evolution of specimens' DNA quality. DNA extraction yield, purity, visual integrity and qualitative and quantitative ability to amplify the Cox1 gene were assessed. Our results show that both RCL2 and ethanol exhibit better performances than formalin. They do not impair DNA extraction yield, and more importantly, DNA alteration is delayed over the preservation step. The use of RCL2 or ethanol as fixative in biological collections may insure a better exploitation of the genetic resources they propose.
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Affiliation(s)
- Emeline Sarot
- INSERM-UMR1037, Université de Toulouse, Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer (LabEx TOUCAN), 31037, Toulouse, France
| | | | - Francis Duranthon
- Muséum d'Histoire Naturelle de Toulouse, 35 allées Jules Guesde, 31000, Toulouse, France
| | - Amandine Péquignot
- Patrimoine Locaux et Gouvernance, UMR208, Muséum national d'Histoire naturelle, 36 rue Geoffroy Saint Hilaire, 75005, Paris, France
| | - Stéphane Pyronnet
- INSERM-UMR1037, Université de Toulouse, Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer (LabEx TOUCAN), 31037, Toulouse, France.
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9
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Benson EE, Harding K, Mackenzie-dodds J. A new quality management perspective for biodiversity conservation and research: Investigating Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) using Natural History Museum and culture collections as case studies. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1201167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Erica E. Benson
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Keith Harding
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Jacqueline Mackenzie-dodds
- Molecular Collections, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Skourtanioti E, Kapli P, Ilgaz Ç, Kumlutaş Y, Avcı A, Ahmadzadeh F, Crnobrnja-Isailović J, Gherghel I, Lymberakis P, Poulakakis N. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes. Mol Phylogenet Evol 2016; 103:199-214. [PMID: 27404043 DOI: 10.1016/j.ympev.2016.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 02/25/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East.
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Affiliation(s)
- Eirini Skourtanioti
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Paschalia Kapli
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, TR-35160, Buca-İzmir, Turkey
| | - Aziz Avcı
- Adnan Menderes University, Faculty of Science and Arts, Department of Biology, 09010 Aydın, Turkey
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Jelka Crnobrnja-Isailović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, Niš 18000, Serbia; Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", Despota Stefana 142, Beograd 11000, Serbia
| | - Iulian Gherghel
- Department of Biology, Case Western Reserve University, 2080 Adelbert Road, Cleveland 44106, Ohio, USA
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, GR-71409 Herakleio, Crete, Greece; Biology Department, School of Sciences and Engineering, University of Crete, Vassilika Vouton, GR-70013 Herakleio, Crete, Greece.
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11
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McCormack JE, Tsai WLE, Faircloth BC. Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Resour 2015; 16:1189-203. [PMID: 26391430 DOI: 10.1111/1755-0998.12466] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/19/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023]
Abstract
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.
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Affiliation(s)
- John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
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12
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Melville J, Smith K, Hobson R, Hunjan S, Shoo L. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia. PLoS One 2014; 9:e101847. [PMID: 25076129 PMCID: PMC4116116 DOI: 10.1371/journal.pone.0101847] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022] Open
Abstract
Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museum Victoria, Melbourne, Victoria, Australia
- * E-mail:
| | - Katie Smith
- Department of Sciences, Museum Victoria, Melbourne, Victoria, Australia
| | - Rod Hobson
- Queensland Parks & Wildlife Service, Toowoomba, Queensland, Australia
| | - Sumitha Hunjan
- Department of Sciences, Museum Victoria, Melbourne, Victoria, Australia
| | - Luke Shoo
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
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13
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Unraveling natural versus anthropogenic effects on genetic diversity within the southeastern beach mouse (Peromyscus polionotus niveiventris). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0417-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Schmitt EM, Glaubrecht M. Revisiting the “Ralum Project”: Molluscs collected by Friedrich Dahl in 1896-1897 for the Museum of Natural History Berlin. ZOOSYST EVOL 2012. [DOI: 10.1002/zoos.201200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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15
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Jackson JA, Laikre L, Baker CS, Kendall KC. Guidelines for collecting and maintaining archives for genetic monitoring. CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9545-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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16
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Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, Bi K, Moritz CC. Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Mol Ecol Resour 2011; 11:1082-92. [PMID: 21791033 DOI: 10.1111/j.1755-0998.2011.03052.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.
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Affiliation(s)
- Kevin C Rowe
- Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001, Australia.
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17
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Farrington HL, Petren K. A century of genetic change and metapopulation dynamics in the Galápagos warbler finches (Certhidea). Evolution 2011; 65:3148-61. [PMID: 22023582 DOI: 10.1111/j.1558-5646.2011.01385.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1894-1906) to modern (1988-2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin's finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad-scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6-8%) as have immigration rates (8-16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18-19%) and also substantial gains (18-20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.
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Affiliation(s)
- Heather L Farrington
- Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA.
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18
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Bluemel JK, Andrew King R, Virant-Doberlet M, Symondson WOC. Primers for identification of type and other archived specimens of Aphrodes leafhoppers (Hemiptera, Cicadellidae). Mol Ecol Resour 2011; 11:770-4. [PMID: 21457478 DOI: 10.1111/j.1755-0998.2011.03008.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Primers were developed for leafhoppers of the genus Aphrodes amplifying 84-244 bp fragments of the mitochondrial cytochrome oxidase subunit I gene. DNA was extracted from legs of over 100-year-old archived museum specimens, amplified and sequenced. The fragments contain sufficient variation to unequivocally identify the different species. The majority of the analysed museum specimens, including three specimens of the syntype series for the UK endemic species A. aestuarina (Edwards 1908), were found to have been assigned to the wrong species. This work clearly underlines the need to validate museum specimens using molecular methods where identity is in doubt, based on reliable standards for species discrimination.
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Affiliation(s)
- Joanna K Bluemel
- Cardiff School of Biosciences, Cardiff University, Biomedical Sciences Building, Museum Avenue, Cardiff CF103AX, UK.
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19
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Historic DNA reveals contemporary population structure results from anthropogenic effects, not pre-fragmentation patterns. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0158-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Gaubert P, Zenatello M. Ancient DNA perspective on the failed introduction of mongooses in Italy during the XXth century. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00614.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Gaubert
- UMR BOREA IRD 207, Muséum National d'Histoire Naturelle, Paris, France
| | - M. Zenatello
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia (BO), Italy
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POULAKAKIS NIKOS, ANTONIOU AGLAIA, MANTZIOU GEORGIA, PARMAKELIS ARIS, SKARTSI THEODORA, VASILAKIS DIMITRIS, ELORRIAGA JAVIER, DE LA PUENTE JAVIER, GAVASHELISHVILI ALEXANDER, GHASABYAN MAMIKON, KATZNER TODD, MCGRADY MICHAEL, BATBAYAR NYAMBAYAR, FULLER MARK, NATSAGDORJ TSEVEENMYADAG. Population structure, diversity, and phylogeography in the near-threatened Eurasian black vultures Aegypius monachus (Falconiformes; Accipitridae) in Europe: insights from microsatellite and mitochondrial DNA variation. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01099.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Diversification patterns of pebble-mimic dragons are consistent with historical disruption of important habitat corridors in arid Australia. Mol Phylogenet Evol 2008; 48:528-42. [DOI: 10.1016/j.ympev.2008.03.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 03/05/2008] [Accepted: 03/13/2008] [Indexed: 11/19/2022]
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23
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STUART BRYANL, FRITZ UWE. Historical DNA from museum type specimens clarifies diversity of Asian leaf turtles (Cyclemys). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.00966.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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POULAKAKIS NIKOS, SFENTHOURAKIS SPYROS. Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences. Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2007.00378.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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