1
|
Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
Collapse
Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
| |
Collapse
|
2
|
Majoros SE, Adamowicz SJ. Phylogenetic signal of sub-arctic beetle communities. Ecol Evol 2022; 12:e8520. [PMID: 35222946 PMCID: PMC8848465 DOI: 10.1002/ece3.8520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022] Open
Abstract
Postglacial dispersal and colonization processes have shaped community patterns in sub-Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub-Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family-level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub-Arctic.
Collapse
|
3
|
Talavera G, Lukhtanov V, Pierce NE, Vila R. DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies. Syst Biol 2021; 71:382-395. [PMID: 34022059 PMCID: PMC8830075 DOI: 10.1093/sysbio/syab038] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/04/2022] Open
Abstract
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]
Collapse
Affiliation(s)
- Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, United States
| | - Vladimir Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, United States
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta, 08003 Barcelona, Catalonia, Spain
| |
Collapse
|
4
|
Cryptic Diversity in the Monotypic Neotropical Micromoth Genus Angelabella (Lepidoptera: Gracillariidae) in the Peru-Chile Desert. INSECTS 2020; 11:insects11100677. [PMID: 33036122 PMCID: PMC7601689 DOI: 10.3390/insects11100677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary The Neotropical Region harbors a highly diverse and poorly known fauna of leaf miners of the micromoth family Gracillariidae (Lepidoptera). Angelabella is a genus of Gracillariidae whose geographic range is restricted to a few valleys of the arid environments of the Peru-Chile desert. Only one species is currently included in this genus. The aims of this study were to explore the geographic range, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses in Angelabella. The spatial distribution of genetic diversity indicated four spatial clusters, three of which are north of the previously known geographic range. These groups were defined as different species by four species delimitation methods. These results suggest that Angelabella harbors at least four morphologically cryptic species with restricted, not overlapping geographic ranges. This study shows that adequate single locus sequence analysis can be useful to discover surprising biodiversity patterns in underexplored environments, providing the base to plan further studies involving little-known organisms. Abstract Angelabella (Lepidoptera: Gracillariidae: Oecophyllembiinae) is considered a monotypic Neotropical genus of leaf miner micromoths known only from a few valleys of the arid environments of the Peru-Chile desert, particularly the southernmost part of Peru and northernmost part of Chile (type locality), where natural populations of its primary host plant occur. The geographic distribution of potential host plants provides a scenario for a wider range for this micromoth genus. The aims of this study were to explore the geographic range of Angelabella, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses. The spatial distribution of genetic diversity indicated the presence of four spatial clusters, three of which are north of the previously known geographic range. Genetic distances were 0.2–0.8% and 3.6–8.3% (K2P) between haplotypes of the same and different spatial clusters, respectively. Phylogenetic relationships indicated reciprocal monophyly among the four spatial clusters, suggesting that allopatric differentiation processes have governed the recent history of Angelabella in these arid environments. These groups were defined as different species by four species delimitation methods, suggesting that Angelabella is not a monotypic genus, but harbors at least four morphologically cryptic allopatric species with restricted geographic ranges, including the type species and three candidate species.
Collapse
|
5
|
Dornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Syst Biol 2018; 68:145-156. [PMID: 29939341 DOI: 10.1093/sysbio/syy047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023] Open
Abstract
With the rise of genome-scale data sets, there has been a call for increased data scrutiny and careful selection of loci that are appropriate to use in an attempt to resolve a phylogenetic problem. Such loci should maximize phylogenetic information content while minimizing the risk of homoplasy. Theory posits the existence of characters that evolve at an optimum rate, and efforts to determine optimal rates of inference have been a cornerstone of phylogenetic experimental design for over two decades. However, both theoretical and empirical investigations of optimal rates have varied dramatically in their conclusions: spanning no relationship to a tight relationship between the rate of change and phylogenetic utility. Herein, we synthesize these apparently contradictory views, demonstrating both empirical and theoretical conditions under which each is correct. We find that optimal rates of characters-not genes-are generally robust to most experimental design decisions. Moreover, consideration of site rate heterogeneity within a given locus is critical to accurate predictions of utility. Factors such as taxon sampling or the targeted number of characters providing support for a topology are additionally critical to the predictions of phylogenetic utility based on the rate of character change. Further, optimality of rates and predictions of phylogenetic utility are not equivalent, demonstrating the need for further development of comprehensive theory of phylogenetic experimental design. [Divergence time; GC bias; homoplasy; incongruence; information content; internode length; optimal rates; phylogenetic informativeness; phylogenetic theory; phylogenetic utility; phylogenomics; signal and noise; subtending branch length; state space; taxon and character sampling.].
Collapse
Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, 1671 Goldstar Drive, NC 27601, USA
| | - Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, 165 Prospect Street, CT 06525, USA
- Department of Biostatistics, Yale University, New Haven, 60 College Street, CT 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, 300 George Street, CT 06511, USA
| |
Collapse
|
6
|
Gibson DJ, Adamowicz SJ, Jacobs SR, Smith MA. Host Specificity in Subarctic Aphids. ENVIRONMENTAL ENTOMOLOGY 2018; 47:77-86. [PMID: 29186477 DOI: 10.1093/ee/nvx176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plants and herbivorous (or parasitic) insects form the majority of macroscopic life. The specificity of interaction between host plant and parasitic insect depends on the adaptations of both the host and the parasite. Over time, these interactions evolve and change as a result of an 'arms race' between host and parasite, and the resulting species-specific adaptations may be maintained, perpetuating these interactions across speciation events. This can lead to specialisation between species or clades. With speciation and species sorting over time, complex interactions evolve. Here, we elucidate a three-tier method to test these interactions using the aphids (Hemiptera: Aphididae) and plants of Churchill (Manitoba, Canada) as a model system. We analyzed these interactions by testing for three patterns in host specificity: monophagy, phylogenetic clustering, and cophylogeny. We defined monophagy strictly as one species feeding exclusively upon a single host plant species (an association likely driven by arms races in morphology, chemical resistance/tolerance, and visual appearance) and observed this in 7 of 22 aphid species. In all the remaining 'polyphagous' cases, there was a strong trend toward monophagy (80% of individuals were found on a single host plant species). Second, we observed two separate examples of phylogenetic clustering where groups of closely related aphid species fed upon individual plant species. Finally, we found no support for cophylogenetic relationships where both aphids and plants cospeciate to form congruent phylogenetic trees (evidence of coadaptation through an ongoing arms race). One explanation for uncovering species-specific interactions in a recently deglaciated, subarctic locality is that the species involved in the associations moved north together. Testing different levels of specificity in the most predominant species-species interactions on the planet will allow us to elucidate these patterns accurately and gives us insight into where to direct future research.
Collapse
Affiliation(s)
- Daniel J Gibson
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Churchill Northern Studies Centre, Manitoba, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shoshanah R Jacobs
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
7
|
Borrelli C, Hou Y, Pawlowski JW, Holzmann M, Katz ME, Chandler GT, Bowser SS. Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata. J Eukaryot Microbiol 2017; 65:220-235. [PMID: 28865158 DOI: 10.1111/jeu.12471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/07/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022]
Abstract
The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (KY468817-KY468826) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).
Collapse
Affiliation(s)
- Chiara Borrelli
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, 12180, New York, USA
| | - Yubo Hou
- Wadsworth Center, New York State Department of Health, Albany, 12201, New York, USA
| | - Jan W Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, 1211, Switzerland
| | - Maria Holzmann
- Department of Genetics and Evolution, University of Geneva, Geneva, 1211, Switzerland
| | - Miriam E Katz
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, 12180, New York, USA
| | - G Thomas Chandler
- Arnold School of Public Health, University of South Carolina, Columbia, 29208, South Carolina, USA
| | - Samuel S Bowser
- Wadsworth Center, New York State Department of Health, Albany, 12201, New York, USA
| |
Collapse
|
8
|
Vamosi JC, Gong YB, Adamowicz SJ, Packer L. Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry. THE NEW PHYTOLOGIST 2017; 214:11-18. [PMID: 27901268 DOI: 10.1111/nph.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.
Collapse
Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
| |
Collapse
|
9
|
Winkler IS, Blaschke JD, Davis DJ, Stireman JO, O'Hara JE, Cerretti P, Moulton JK. Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae). Mol Phylogenet Evol 2015; 88:38-54. [PMID: 25841383 DOI: 10.1016/j.ympev.2015.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 12/01/2022]
Abstract
Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and their relatives, we show that a small number of well-chosen nuclear protein-coding genes can successfully resolve even difficult phylogenetic problems.
Collapse
Affiliation(s)
- Isaac S Winkler
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA; Department of Biology, Linfield College, McMinnville, OR 97128, USA
| | - Jeremy D Blaschke
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel J Davis
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | - John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - James E O'Hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Pierfilippo Cerretti
- DAFNAE-Entomology, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (Padova), Italy; Dipartimento di Biologia e Biotecnologie 'Charles Darwin', 'Sapienza' Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
10
|
Jin Q, Han H, Hu X, Li X, Zhu C, Ho SYW, Ward RD, Zhang AB. Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau. PLoS One 2013; 8:e64428. [PMID: 23741330 PMCID: PMC3669328 DOI: 10.1371/journal.pone.0064428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/14/2013] [Indexed: 12/18/2022] Open
Abstract
With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.
Collapse
Affiliation(s)
- Qian Jin
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - Huilin Han
- School of Forestry, Experiment Center, Northeast Forestry University, Haerbin, People's Republic of China
| | - XiMin Hu
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| | - XinHai Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - ChaoDong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Simon Y. W. Ho
- School of Biological Sciences, University Of Sydney, Sydney, Australia
| | - Robert D. Ward
- Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, Hobart, Tasmania, Australia
| | - Ai-bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, People's Republic of China
| |
Collapse
|
11
|
Nagy ZT, Sonet G, Glaw F, Vences M. First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS One 2012; 7:e34506. [PMID: 22479636 PMCID: PMC3316696 DOI: 10.1371/journal.pone.0034506] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/02/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar. METHODOLOGY/PRINCIPAL FINDINGS Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family. CONCLUSIONS/SIGNIFICANCE The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.
Collapse
Affiliation(s)
- Zoltán T Nagy
- Joint Experimental Molecular Unit, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.
| | | | | | | |
Collapse
|