1
|
Qu J, Lu X, Teng X, Xing Z, Wang S, Feng C, Wang X, Wang L. Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny. Animals (Basel) 2024; 14:2220. [PMID: 39123752 PMCID: PMC11310995 DOI: 10.3390/ani14152220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management.
Collapse
Affiliation(s)
- Jiangyong Qu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xiaofei Lu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao 266071, China;
| | - Zhikai Xing
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Shuang Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Chunyu Feng
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xumin Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Lijun Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Kneubehl AR, Muñoz-Leal S, Filatov S, de Klerk DG, Pienaar R, Lohmeyer KH, Bermúdez SE, Suriyamongkol T, Mali I, Kanduma E, Latif AA, Sarih M, Bouattour A, de León AAP, Teel PD, Labruna MB, Mans BJ, Lopez JE. Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis. Sci Rep 2022; 12:19310. [PMID: 36369253 PMCID: PMC9652274 DOI: 10.1038/s41598-022-23393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks. However, current methods to generate mitogenomes can be cost-prohibitive at scale. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies' Mk1B sequencer. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. This cost-effective strategy is applicable for sample identification, taxonomy, systematics, and population genetics for not only ticks but likely other metazoans; thus, making mitogenome sequencing equitable for the wider scientific community.
Collapse
Affiliation(s)
- Alexander R Kneubehl
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Sebastián Muñoz-Leal
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Serhii Filatov
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Daniel G de Klerk
- Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Ronel Pienaar
- Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Kimberly H Lohmeyer
- Knipling-Bushland U.S. Livestock Insects Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Kerrville, TX, USA
| | - Sergio E Bermúdez
- Medical Entomology Department, Gorgas Memorial Institute for Health Research, City of Panamá, Panama
| | - Thanchira Suriyamongkol
- Department of Biology, Eastern New Mexico University, Portales, NM, USA.,Southern Illinois University-Carbondale, Cooperative Wildlife Research Laboratory, Carbondale, IL, USA
| | - Ivana Mali
- Fisheries, Wildlife, and Conservation Biology Program, North Carolina State University, Raleigh, USA
| | - Esther Kanduma
- Department of Biochemistry, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Abdalla A Latif
- University of KwaZulu-Natal, School of Life Sciences, Durban, Westville, South Africa
| | - M'hammed Sarih
- Institut Pasteur du Maroc, Service de Parasitologie et des Maladies Vectorielles, Casablanca, Morocco
| | - Ali Bouattour
- Institut Pasteur de Tunis, Université Tunis El Manar, Laboratoire Virus, Vecteurs, Hôtes, Service d'Entomologie Médicale, Tunis, Tunisia
| | - Adalberto A Pérez de León
- San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA, USA
| | - Pete D Teel
- Department of Entomology, Texas A&M AgriLife Research, College Station, TX, USA
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Ben J Mans
- Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa.,Department of Life and Consumer Sciences, University of South Africa, Pretoria, South Africa.,Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Job E Lopez
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
4
|
Roycroft E, Moritz C, Rowe KC, Moussalli A, Eldridge MDB, Portela Miguez R, Piggott MP, Potter S. Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.931644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.
Collapse
|
5
|
Zheng B, Han Y, Yuan R, Liu J, Tang P, van Achterberg C, Chen X. Mitochondrial Genomes Yield Insights into the Basal Lineages of Ichneumonid Wasps (Hymenoptera: Ichneumonidae). Genes (Basel) 2022; 13:genes13020218. [PMID: 35205263 PMCID: PMC8872219 DOI: 10.3390/genes13020218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
We obtained four mitochondrial genomes of Odontocolon sp., Xorides funiuensis, Euceros kiushuensis and Euceros serricornis, which represent the first two representatives from subfamily Eucerotinae and Xoridinae (Ichneumonidae), respectively. All of the 4 newly sequenced mitochondrial genomes contain 13 protein-coding genes (PCGs) and most 24 RNA genes. Furthermore, they all have novel tRNA rearrangement patterns comparing with published mitogenomes in Ichneumonidae. For the tRNA cluster trnI-trnQ-trnM, X. funiuensis is shuffled as trnM-trnI-trnQ with trnQ inversed, while Odontocolon sp. with a remote translocation of trnK, shuffling as trnI-trnM-trnQ. E. kiushuensis and E. serricornis shared the same cluster trnQ-trnY-trnW-trnC. Finally, we reconstructed the phylogenetic relationships among the sequenced subfamilies of Ichneumonidae based on nucleotides and amino acids sequences of 13 PCGs in mitochondrial genomes, and the results of both the maximum likelihood and Bayesian inference analyses highly support that Eucerotinae is the basal ichneumonid lineage rather than Xoridinae.
Collapse
Affiliation(s)
- Boying Zheng
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Han
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ruizhong Yuan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingxian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
| | - Pu Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Cornelis van Achterberg
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuexin Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
6
|
Zheng B, Han Y, Yuan R, Liu J, van Achterberg C, Tang P, Chen X. Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny. INSECTS 2022; 13:insects13020124. [PMID: 35206698 PMCID: PMC8874624 DOI: 10.3390/insects13020124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Nearly a hundred mitochondrial genomes of ichneumonid wasps are newly reported. Comparative mitogenomics of 104 mitochondrial genomes representing 33 subfamilies of Ichneumonidae, as well as its implications for phylogeny, were studied. We found that the mitochondrial genomes of ichneumonid wasps were highly conserved in their base composition and had low evolutionary rates, but were diverse in gene order. There are 38 types of gene rearrangement events in 104 ichneumonid mitochondrial genomes, of which 30 novel rearrangement types (R3-6, R8-R10, R12-R15, R17-R18, R20-R35 and R38) and a hot spot rearrangement around R1, with a shuffled tRNA cluster trnW-trnY-trnC and trnI-trnQ-trnM, were detected. The relationships among these subfamilies are firstly discussed based on mitochondrial genomes at a large scale. We suggest five subfamily groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. Abstract Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.
Collapse
Affiliation(s)
- Boying Zheng
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Han
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ruizhong Yuan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingxian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
| | - Cornelis van Achterberg
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Xuexin Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
Collapse
Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| |
Collapse
|
9
|
Kirchhof S, Lyra ML, Rodríguez A, Ineich I, Müller J, Rödel MO, Trape JF, Vences M, Boissinot S. Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophile lizard genus Acanthodactylus. Sci Rep 2021; 11:4858. [PMID: 33649347 PMCID: PMC7921649 DOI: 10.1038/s41598-021-83422-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022] Open
Abstract
Climate has a large impact on diversity and evolution of the world's biota. The Eocene-Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene-Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them-and especially A. guineensis-as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene-Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.
Collapse
Affiliation(s)
- Sebastian Kirchhof
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates.
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, CEP 13506-900, Brazil
| | - Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Ivan Ineich
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, CP 30, 57 rue Cuvier, 75005, Paris, France
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jean-François Trape
- Laboratoire de Paludologie et Zoologie médicale, IRD, UMR MIVEGEC, B. P. 1386, Dakar, Senegal
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Stéphane Boissinot
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates
| |
Collapse
|
10
|
Incorporating RDA Outputs in the Design of a European Research Infrastructure for Natural Science Collections. DATA SCIENCE JOURNAL 2020. [DOI: 10.5334/dsj-2020-050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
11
|
Wu MY, Low GW, Forcina G, van Grouw H, Lee BPYH, Oh RRY, Rheindt FE. Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evol Appl 2020; 13:2300-2315. [PMID: 33005225 PMCID: PMC7513718 DOI: 10.1111/eva.13023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023] Open
Abstract
The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110-150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral-wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
Collapse
Affiliation(s)
- Meng Yue Wu
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Gabriel Weijie Low
- Department of Biological Sciences National University of Singapore Singapore Singapore
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Giovanni Forcina
- Department of Biological Sciences National University of Singapore Singapore Singapore
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Hein van Grouw
- Bird Group Department of Life Sciences Natural History Museum Herts UK
| | - Benjamin P Y-H Lee
- Wildlife Management Research Wildlife Management Division National Parks Board Singapore Singapore
| | - Rachel Rui Ying Oh
- Centre of Urban Greenery and Ecology National Parks Board Singapore Singapore
- School of Biological Sciences Centre for Biodiversity and Conservation Sciences University of Queensland Brisbane Queensland Australia
| | - Frank E Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| |
Collapse
|
12
|
Mudge C, Dallwitz R, Llamas B, Austin JJ. Using Ancient DNA Analysis and Radiocarbon Dating to Determine the Provenance of an Unusual Whaling Artifact. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.505233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
13
|
Parejo M, Wragg D, Henriques D, Charrière JD, Estonba A. Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens. Genome Biol Evol 2020; 12:2535-2551. [PMID: 32877519 PMCID: PMC7720081 DOI: 10.1093/gbe/evaa188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 11/20/2022] Open
Abstract
Historical specimens in museum collections provide opportunities to gain insights into the genomic past. For the Western honey bee, Apis mellifera L., this is particularly important because its populations are currently under threat worldwide and have experienced many changes in management and environment over the last century. Using Swiss Apis mellifera mellifera as a case study, our research provides important insights into the genetic diversity of native honey bees prior to the industrial-scale introductions and trade of non-native stocks during the 20th century—the onset of intensive commercial breeding and the decline of wild honey bees following the arrival of Varroa destructor. We sequenced whole-genomes of 22 honey bees from the Natural History Museum in Bern collected in Switzerland, including the oldest A. mellifera sample ever sequenced. We identify both, a historic and a recent migrant, natural or human-mediated, which corroborates with the population history of honey bees in Switzerland. Contrary to what we expected, we find no evidence for a significant genetic bottleneck in Swiss honey bees, and find that genetic diversity is not only maintained, but even slightly increased, most probably due to modern apicultural practices. Finally, we identify signals of selection between historic and modern honey bee populations associated with genes enriched in functions linked to xenobiotics, suggesting a possible selective pressure from the increasing use and diversity of chemicals used in agriculture and apiculture over the last century.
Collapse
Affiliation(s)
- Melanie Parejo
- Agroscope, Swiss Bee Research Center, Bern, Switzerland.,Lab. Genetics, Department of Genetics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - David Wragg
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Dora Henriques
- Instituto Politécnico de Bragança, Centro de Investigação de Montanha (CIMO), Bragança, Portugal
| | | | - Andone Estonba
- Lab. Genetics, Department of Genetics, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| |
Collapse
|
14
|
Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
Collapse
Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Lavretsky P, McInerney NR, Mohl JE, Brown JI, James HF, McCracken KG, Fleischer RC. Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks. Mol Ecol 2020; 29:578-595. [PMID: 31872482 DOI: 10.1111/mec.15343] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.
Collapse
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Nancy Rotzel McInerney
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Jonathon E Mohl
- Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, USA
| | - Joshua I Brown
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin G McCracken
- Department of Biology, University of Miami, Coral Gables, FL, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.,Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Institute of Arctic Biology, University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
17
|
Tsai WLE, Schedl ME, Maley JM, McCormack JE. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol Ecol Resour 2019; 20:1220-1227. [PMID: 31478338 DOI: 10.1111/1755-0998.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
Collapse
Affiliation(s)
- Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Margaret E Schedl
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California.,Biology Department, Occidental College, Los Angeles, California
| |
Collapse
|
18
|
Billerman SM, Walsh J. Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions. Mol Ecol Resour 2019; 19:1115-1130. [PMID: 31336408 DOI: 10.1111/1755-0998.13066] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high-throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.
Collapse
Affiliation(s)
- Shawn M Billerman
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
19
|
Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
Collapse
Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| |
Collapse
|
20
|
Tsai WL, Mota-Vargas C, Rojas-Soto O, Bhowmik R, Liang EY, Maley JM, Zarza E, McCormack JE. Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands. Mol Phylogenet Evol 2019; 136:29-34. [DOI: 10.1016/j.ympev.2019.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/22/2019] [Indexed: 11/28/2022]
|
21
|
A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes. Mol Phylogenet Evol 2018; 129:304-314. [DOI: 10.1016/j.ympev.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/23/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022]
|
22
|
Greiman SE, Cook JA, Tkach VV, Hoberg EP, Menning DM, Hope AG, Sonsthagen SA, Talbot SL. Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time. Int J Parasitol 2018; 48:1061-1070. [PMID: 30315762 DOI: 10.1016/j.ijpara.2018.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/02/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at -80 °C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.
Collapse
Affiliation(s)
- Stephen E Greiman
- Department of Biology, Georgia Southern University, 4324 Old Register Rd., Statesboro, GA 30460, USA; Department of Biology and Museum of Southwestern Biology, University of New Mexico, CERIA, 302 Yale Blvd NE, Albuquerque, NM 87106, USA.
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, CERIA, 302 Yale Blvd NE, Albuquerque, NM 87106, USA
| | - Vasyl V Tkach
- Department of Biology, University of North Dakota, 10 Cornell St., Grand Forks 58202, ND, USA
| | - Eric P Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, CERIA, 302 Yale Blvd NE, Albuquerque, NM 87106, USA
| | - Damian M Menning
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Andrew G Hope
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Sarah A Sonsthagen
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| | - Sandra L Talbot
- US Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508, USA
| |
Collapse
|
23
|
ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
|
24
|
Vu CM, Piniewski DW, McLean OA, McCabe DJ. Use of Point-and-Shoot Photography to Compare Regional Differences inCanis latrans(Coyote) Skull Size. Northeast Nat (Steuben) 2018. [DOI: 10.1656/045.025.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Catherine M.T. Vu
- Biology Box 283, Saint Michael's College, One Winooski Park, Colchester, VT 05439
| | - Devan W. Piniewski
- Biology Box 283, Saint Michael's College, One Winooski Park, Colchester, VT 05439
| | - Osrica A.P. McLean
- Biology Box 283, Saint Michael's College, One Winooski Park, Colchester, VT 05439
| | - Declan J. McCabe
- Biology Box 283, Saint Michael's College, One Winooski Park, Colchester, VT 05439
| |
Collapse
|
25
|
Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
|
26
|
Tan MH, Gan HM, Dally G, Horner S, Moreno PAR, Rahman S, Austin CM. More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae). INVERTEBR SYST 2018. [DOI: 10.1071/is17050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.
Collapse
|
27
|
Grant T, Rada M, Anganoy-Criollo M, Batista A, Dias PH, Jeckel AM, Machado DJ, Rueda-Almonacid JV. Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea). SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2017. [DOI: 10.2994/sajh-d-17-00017.1] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Amphibian Collection, Museum of Zoology of the University of São Paulo, 04263-000, São Paulo, SP, Brazil
| | - Marco Rada
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Marvin Anganoy-Criollo
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Abel Batista
- Universidad Autónoma de Chiriquí, David, Republic of Panama
- Los Naturalistas, David 0426-01459, Chiriquí, Panama
| | - Pedro Henrique Dias
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Adriana Moriguchi Jeckel
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | | |
Collapse
|
28
|
Linck EB, Hanna ZR, Sellas A, Dumbacher JP. Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecol Evol 2017; 7:4755-4767. [PMID: 28690805 PMCID: PMC5496524 DOI: 10.1002/ece3.3065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.
Collapse
Affiliation(s)
- Ethan B. Linck
- Department of BiologyBurke Museum of Natural History & CultureUniversity of WashingtonSeattleWAUSA
| | - Zachary R. Hanna
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCAUSA
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCAUSA
- Ornithology & MammologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Anna Sellas
- Center for Comparative GenomicsCalifornia Academy of SciencesSan FranciscoCAUSA
| | - John P. Dumbacher
- Ornithology & MammologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Center for Comparative GenomicsCalifornia Academy of SciencesSan FranciscoCAUSA
| |
Collapse
|
29
|
Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T, Distefano RJ, Blaha M, Roles AJ, Austin CM. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. ZOOL SCR 2017. [DOI: 10.1111/zsc.12247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederic Grandjean
- UMR CNRS 7267 Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions; 5 rue Albert Turpin Poitiers Cedex France
| | - Mun Hua Tan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Han Ming Gan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Yin Peng Lee
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
| | - Tadashi Kawai
- Fisheries Research Department; Wakkanai Fisheries Research Institute; 4-5-15 Suehiro Wakkanai-shi 097-0001 Hokkaido Japan
| | - Robert J. Distefano
- Missouri Department of Conservation; East Gans Road Columbia Missouri 65201 USA
| | - Martin Blaha
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Zátiší 728/II Vodňany Czech Republic
| | - Angela J. Roles
- Biology Department; Oberlin College, Oberlin; Ohio 44074 USA
| | - Christopher M. Austin
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| |
Collapse
|
30
|
Sproul JS, Maddison DR. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded
DNA. Mol Ecol Resour 2017; 17:1183-1201. [DOI: 10.1111/1755-0998.12660] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/28/2022]
Affiliation(s)
- John S. Sproul
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
| | - David R. Maddison
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
| |
Collapse
|
31
|
Haponski AE, Lee T, Ó Foighil D. Moorean and Tahitian Partula tree snail survival after a mass extinction: New genomic insights using museum specimens. Mol Phylogenet Evol 2017; 106:151-157. [DOI: 10.1016/j.ympev.2016.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/15/2016] [Accepted: 09/23/2016] [Indexed: 11/16/2022]
|
32
|
Martínez-Aquino A, Vigliano-relva J, Brusa F, Damborenea C. Historical biogeography of Temnocephalida (Platyhelminthes, Rhabdocoela): testing the Gondwanan hypothesis. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1252441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Andres Martínez-Aquino
- Laboratorio de Patología Acuática, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Km 6 Carretera Antigua a Progreso, Cordemex, Mérida, Yucatán 97310, México
| | - Julieta Vigliano-relva
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
| | - Francisco Brusa
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Cristina Damborenea
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| |
Collapse
|
33
|
Anmarkrud JA, Lifjeld JT. Complete mitochondrial genomes of eleven extinct or possibly extinct bird species. Mol Ecol Resour 2016; 17:334-341. [DOI: 10.1111/1755-0998.12600] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 08/18/2016] [Accepted: 09/16/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jarl A. Anmarkrud
- Natural History Museum University of Oslo PO Box 1172 Blindern Oslo 0318 Norway
| | - Jan T. Lifjeld
- Natural History Museum University of Oslo PO Box 1172 Blindern Oslo 0318 Norway
| |
Collapse
|
34
|
Besnard G, Thèves C, Mata X, Holota H, Rakotozafy LMA, Pedrono M. Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4543-4544. [PMID: 27159683 DOI: 10.3109/19401736.2015.1101554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.
Collapse
Affiliation(s)
| | - Catherine Thèves
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Xavier Mata
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Hélène Holota
- a Laboratoire EDB , UMR5174, CNRS-UPS-ENFA , Toulouse , France
| | - Lucien M A Rakotozafy
- c Laboratoire de Zooarchéologie , Institut des Civilisations, Musée d'Art et d'Archéologie de l'Université d'Antananarivo , Antananarivo , Madagascar
| | - Miguel Pedrono
- d CIRAD, UPR AGIRs , Antananarivo , Madagascar.,e CIRAD, UPR AGIRs, Campus International de Baillarguet , Montpellier , France
| |
Collapse
|
35
|
Gold MEL, Bourdon E, Norell MA. The first endocast of the extinct dodo (Raphus cucullatus) and an anatomical comparison amongst close relatives (Aves, Columbiformes). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12388] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Maria Eugenia Leone Gold
- Richard Gilder Graduate School; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
- Division of Paleontology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
- Department of Anatomical Sciences; Stony Brook University; Health Sciences Center; Stony Brook NY 11794 USA
| | - Estelle Bourdon
- Section of Biosystematics; Natural History Museum of Denmark; University of Copenhagen; Universitetsparken 15 2100 Copenhagen Denmark
| | - Mark A. Norell
- Richard Gilder Graduate School; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
- Division of Paleontology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| |
Collapse
|
36
|
Affiliation(s)
- Sven Buerki
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | | |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12509] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Loubab Zedane
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Cynthia Hong-Wa
- Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
| | - Jérôme Murienne
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Céline Jeziorski
- INRA; UAR1209; département de Génétique Animale; INRA Auzeville 31326; Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville 31326; Castanet-Tolosan France
| | - Bruce G. Baldwin
- Jepson Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| |
Collapse
|