1
|
Samreen KB, Manzoor F. Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan. PeerJ 2024; 12:e17420. [PMID: 38832046 PMCID: PMC11146329 DOI: 10.7717/peerj.17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.
Collapse
Affiliation(s)
- Khush Bakhat Samreen
- Department of Zoology, Lahore College for Women University, Lahore, Lahore, Pakistan
| | | |
Collapse
|
2
|
Paula DP, Andow DA. DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents. NEOTROPICAL ENTOMOLOGY 2023; 52:302-332. [PMID: 36478343 DOI: 10.1007/s13744-022-01011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.
Collapse
|
3
|
Chaiphongpachara T, Changbunjong T, Sumruayphol S, Laojun S, Suwandittakul N, Kuntawong K. Geometric morphometrics versus DNA barcoding for the identification of malaria vectors Anopheles dirus and An. baimaii in the Thai-Cambodia border. Sci Rep 2022; 12:13236. [PMID: 35918453 PMCID: PMC9345986 DOI: 10.1038/s41598-022-17646-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Anopheles (Cellia) dirus Peyton & Harrison and Anopheles baimaii Sallum & Peyton are sibling species within the Dirus complex belonging to the Leucosphyrus group, and have been incriminated as primary vectors of malaria in Thailand. In the present study, DNA barcoding and geometric morphometrics were used to distinguish between An. dirus and An. baimaii in the international border areas, Trat Province, eastern Thailand. Our results revealed that DNA barcoding based on the cytochrome c oxidase subunit I gene could not be used to distinguish An. dirus from An. baimaii. The overlapping values between intra- and interspecific genetic divergence indicated no barcoding gap present for An. dirus and An. baimaii (ranging from 0 to 0.99%). However, the results of the geometric morphometric analysis based on the wing shape clearly distinguished An. dirus and An. baimaii, with 92.42% of specimens assigned to the correct species. We concluded that geometric morphometrics is an effective tool for the correct species identification of these two malaria vectors. Our findings could be used to make entomological surveillance information more accurate, leading to further effective mosquito control planning in Thailand and other countries in Southeast Asia.
Collapse
Affiliation(s)
- Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.,The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Suchada Sumruayphol
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Nantana Suwandittakul
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Kewarin Kuntawong
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| |
Collapse
|
4
|
Dooley KE, Niemiller KDK, Sturm N, Niemiller ML. Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.43.79993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Shelta Cave Crayfish (Orconectes sheltae) is a small, cave-obligate member of the genus Orconectes (family Cambaridae) endemic to a single cave system—Shelta Cave—in northwest Huntsville, Madison Co., Alabama, USA. Although never abundant, this stygobiont was regularly observed in the 1960s and early 1970s before the population and aquatic community in general at Shelta Cave collapsed likely in response to groundwater contamination and the loss of energetic inputs from a Grey Bat (Myotis grisescens) maternity colony that abandoned the cave after installation of a poorly designed cave gate. We conducted 20 visual surveys of aquatic habitats at Shelta Cave between October 2018 and July 2021. Although the aquatic community has not recovered, we did confirm the continued existence of O. sheltae, which had not been observed in 31 years, with observations of an adult female on 31 May 2019 and an adult male on 28 August 2020. We conducted the first phylogenetic analyses of O. sheltae and discovered that the species is most closely related to other geographically proximate stygobiotic crayfishes in the genus Cambarus in northern Alabama than members of the genus Orconectes. We advocate for recognition of this species as Cambarus sheltae to more accurately reflect evolutionary relationships of this single-cave endemic and offer recommendations for its management, conservation, and future research, as this species remains at high risk of extinction.
Collapse
|
5
|
Hlebec D, Sivec I, Podnar M, Kučinić M. DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 2022; 10:e13213. [PMID: 35469200 PMCID: PMC9034701 DOI: 10.7717/peerj.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.
Collapse
Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia,Zoological Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany,Croatian Biospeleological Society, Zagreb, Croatia
| | - Ignac Sivec
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | | | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
6
|
Justine JL, Gastineau R, Gros P, Gey D, Ruzzier E, Charles L, Winsor L. Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte. PeerJ 2022; 10:e12725. [PMID: 35178290 PMCID: PMC8815365 DOI: 10.7717/peerj.12725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/10/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. METHODS Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium "black", and the morphology of a species previously reported as Diversibipalium "blue". Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. RESULTS The new species Humbertium covidum n. sp. (syn: Diversibipalium "black" of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium "blue" of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position. CONCLUSION Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.
Collapse
Affiliation(s)
- Jean-Lou Justine
- ISYEB-Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Paris, France
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Pierre Gros
- Amateur Naturalist, Unaffiliated, Cagnes-sur-Mer, France
| | - Delphine Gey
- Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Paris, France
| | - Enrico Ruzzier
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), Padova, Italy
| | | | - Leigh Winsor
- James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
7
|
Gutierrez MAC, Lopez ROH, Ramos AT, Vélez ID, Gomez RV, Arrivillaga-Henríquez J, Uribe S. DNA barcoding of Lutzomyia longipalpis species complex (Diptera: Psychodidae), suggests the existence of 8 candidate species. Acta Trop 2021; 221:105983. [PMID: 34048789 DOI: 10.1016/j.actatropica.2021.105983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/27/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
The sand fly Lutzomyia (L.) longipalpis has been implicated as the primary vector of Leishmania infantum, the causative agent of visceral leishmaniasis VL. In addition, it has been associated with atypical cutaneous leishmaniasis transmission in the Neotropic and Central America, respectively. The existence of a L. longipalpis complex species has been suggested with important implications for leishmaniasis epidemiology; however, the delimitation of species conforming it remains a topic of controversy. The DNA Barcoding Initiative based on cox1 sequence variation was used to identify the MOTUs in L. longipalpis including previously described L. pseudolongipalpis. The genetic variation was analyzed based on tree and distance methods. Fifty-five haplotypes were obtained from 103 sequences which were assigned to MOTUs, with a clear separation and a high correspondence of individuals to the groups. Maximum likelihood and Bayesian phylogenetic analysis showed eight MOTUs (100% bootstrap) with high genetic divergence (12.6%). Data obtained in the present study suggest that L. longipalpis complex consists of at least 8 lineages that may represent species. It would be desirable perform additional morphological and molecular analysis of L. longipalpis from Colosó (Caribbean ecoregion) considering that specimens from that area were grouped with L. pseudolongipalpis one of the complex species previously described from Venezuela, which has not been registered in Colombia.
Collapse
|
8
|
Abstract
Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.
Collapse
|
9
|
Cardenas CR, Luo AR, Jones TH, Schultz TR, Adams RM. Using an integrative taxonomic approach to delimit a sibling species, Mycetomoellerius mikromelanos sp. nov. (Formicidae: Attini: Attina). PeerJ 2021; 9:e11622. [PMID: 34221725 PMCID: PMC8236233 DOI: 10.7717/peerj.11622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
The fungus-growing ant Mycetomoellerius (previously Trachymyrmex) zeteki (Weber 1940) has been the focus of a wide range of studies examining symbiotic partners, garden pathogens, mating frequencies, and genomics. This is in part due to the ease of collecting colonies from creek embankments and its high abundance in the Panama Canal region. The original description was based on samples collected on Barro Colorado Island (BCI), Panama. However, most subsequent studies have sampled populations on the mainland 15 km southeast of BCI. Herein we show that two sibling ant species live in sympatry on the mainland: Mycetomoellerius mikromelanos Cardenas, Schultz, & Adams and M. zeteki. This distinction was originally based on behavioral differences of workers in the field and on queen morphology (M. mikromelanos workers and queens are smaller and black while those of M. zeteki are larger and red). Authors frequently refer to either species as "M. cf. zeteki," indicating uncertainty about identity. We used an integrative taxonomic approach to resolve this, examining worker behavior, chemical profiles of worker volatiles, molecular markers, and morphology of all castes. For the latter, we used conventional taxonomic indicators from nine measurements, six extrapolated indices, and morphological characters. We document a new observation of a Diapriinae (Hymenoptera: Diapriidae) parasitoid wasp parasitizing M. zeteki. Finally, we discuss the importance of vouchering in dependable, accessible museum collections and provide a table of previously published papers to clarify the usage of the name T. zeteki. We found that most reports of M. zeteki or M. cf. zeteki-including a genome-actually refer to the new species M. mikromelanos.
Collapse
Affiliation(s)
- Cody Raul Cardenas
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| | - Amy Rongyan Luo
- Department of Ecology & Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, United States of America
| | - Tappey H. Jones
- Department of Chemistry, Virginia Military Institute, Lexington, VA, United States of America
| | - Ted R. Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia, United States of America
| | - Rachelle M.M. Adams
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States of America
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia, United States of America
| |
Collapse
|
10
|
Roy L, Giangaspero A, Sleeckx N, Øines Ø. Who Is Dermanyssus gallinae? Genetic Structure of Populations and Critical Synthesis of the Current Knowledge. Front Vet Sci 2021; 8:650546. [PMID: 34124219 PMCID: PMC8194076 DOI: 10.3389/fvets.2021.650546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Despite the economic and animal welfare importance of the Poultry Red Mite Dermanyssus gallinae, its genetic structure has been studied in a scattered way so far. The prophylaxis and control of such a globally distributed ectoparasite can be significantly improved by understanding its genetic population structure (composition in species and intraspecific variants). The present study aims to establish a rigorous framework for characterizing the neutral genetic structure of D. gallinae based on a literature review combined with an integrative analysis of the data available in GenBank on population-level nucleotide sequence diversity supplemented by a new dataset. The integrative analysis was conducted on sequence data extracted from GenBank coupled with new sequences of two fragments of the mitochondrial gene encoding Cytochrome Oxidase I (CO1) as well as of an intron of the nuclear gene encoding Tropomyosin (Tpm) from several PRM populations sampled from European poultry farms. Emphasis was placed on using the mitochondrial gene encoding CO1 on which the main universal region of DNA barcoding in animals is located. The species D. gallinae sensu lato is a species complex, encompassing at least two cryptic species, i.e., not distinguishable by morphological characters: D. gallinae sensu stricto and D. gallinae L1. Only D. gallinae s.s. has been recorded among the populations sampled in poultry farms worldwide. Current knowledge suggests they are structured in three mitochondrial groups (haplogroups A, B, and C). Haplogroup A is cosmopolitan, and the other two present slightly contrasted distributions (B rather in the northern part of Europe, C most frequently found in the southern part). Recent data indicate that a dynamic geographic expansion of haplogroup C is underway in Europe. Our results also show that NUMT (nuclear mitochondrial DNA) pseudogenes have generated artifactual groups (haplogroups E and F). It is important to exclude these artifact groups from future analyses to avoid confusion. We provide an operational framework that will promote consistency in the analysis of subsequent results using the CO1 fragment and recommendations for future analyses.
Collapse
Affiliation(s)
- Lise Roy
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Annunziata Giangaspero
- Department of Agriculture, Food, Natural Resources, and Engineering (DAFNE), University of Foggia, Foggia, Italy
| | | | | |
Collapse
|
11
|
Porter TM, Hajibabaei M. Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 2021; 22:256. [PMID: 34011275 PMCID: PMC8136176 DOI: 10.1186/s12859-021-04180-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. RESULTS Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. CONCLUSIONS Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.
Collapse
Affiliation(s)
- T M Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON, Canada.
| | - M Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| |
Collapse
|
12
|
Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
Collapse
Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| |
Collapse
|
13
|
Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA. Primates 2021; 62:667-675. [PMID: 33909155 DOI: 10.1007/s10329-021-00912-y] [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: 03/06/2020] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations.
Collapse
|
14
|
Uesugi R, Jouraku A, Sukonthabhirom Na Pattalung S, Hinomoto N, Kuwazaki S, Kanamori H, Katayose Y, Sonoda S. Origin, selection, and spread of diamide insecticide resistance allele in field populations of diamondback moth in east and southeast Asia. PEST MANAGEMENT SCIENCE 2021; 77:313-324. [PMID: 33411414 DOI: 10.1002/ps.6020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The investigation of molecular mechanisms and evolution of resistance to insecticides is an ongoing challenge, as researchers must provide guidance to manage the resistance to achieve sustainable production in agriculture. Predicting, monitoring, and managing insecticide resistance requires information on the origins, selection, and spread of resistance genes. The resistance of Plutella xylostella (L.) against diamide insecticides is becoming an increasingly severe problem in east and southeast Asia. In this study, the evolution of resistance was investigated using a resistance allele [ryanodine receptor (RyR); G4946E mutation] and its flanking regions, as well as mitochondrial cytochrome c oxidase subunit I (mtCOI). RESULTS The sequences of the flanking region of the G4946E and mtCOI suggested that the G4946E mutation has a key role in resistance. Furthermore, the G4946E mutation has multiple origins, and congenic resistant mutations have spread across east and southeast Asia, despite substantial geographical barriers. In addition, the susceptibility of field populations partially recovered during winter, based on the observed decrease in the G4946E (resistant allele) frequency. Finally, the resistance level indexed by the frequency of the E4946 allele was significantly lower in non-overwintering regions than in overwintering regions. CONCLUSION The information of the present study is useful to monitor resistance using molecular markers and to develop strategies to delay the evolution of diamide resistance.
Collapse
Affiliation(s)
- Ryuji Uesugi
- Division of Agro-Environment Research, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Iwate, Japan
| | - Akiya Jouraku
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | | | - Norihide Hinomoto
- Department of Applied Entomology and Zoology, Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Seigo Kuwazaki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Hiroyuki Kanamori
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Yuichi Katayose
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shoji Sonoda
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
| |
Collapse
|
15
|
Cho G, Malenovský I, Burckhardt D, Inoue H, Lee S. DNA barcoding of pear psyllids (Hemiptera: Psylloidea: Psyllidae), a tale of continued misidentifications. BULLETIN OF ENTOMOLOGICAL RESEARCH 2020; 110:521-534. [PMID: 32037992 DOI: 10.1017/s0007485320000012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pear psyllids (Hemiptera: Psylloidea: Psyllidae: Cacopsylla spp.) belong to the most serious pests of pear (Pyrus spp.). They damage pear trees by excessive removal of phloem sap, by soiling the fruits with honeydew which, in turn, provides a substrate for sooty mould, and by transmission of Candidatus Phytoplasma spp., the causal agents of the pear decline disease. The morphological similarity, the presence of seasonal dimorphism that affects adult colour, size and wing morphology and uncritical use of species names, led to much confusion in the taxonomy of pear psyllids. As a result, pear psyllids have been frequently misidentified. Many of the entries attributed to Cacopsylla pyricola and other species in the GenBank are misidentifications which led to additional, unnecessary confusion. Here we analysed DNA barcodes of 11 pear psyllid species from eastern Asia, Europe and Iran using four mitochondrial gene fragments (COI 658 bp, COI 403 bp, COI-tRNAleu-COII 580 bp and 16S rDNA 452 bp). The efficiency of identification was notably high and considerable barcoding gaps were observed in all markers. Our results confirm the synonymies of the seasonal forms of Cacopsylla jukyungi ( = C. cinereosignata, winter form) and C. maculatili ( = C. qiuzili, summer form) previously suggested based on morphology. Some previous misidentifications (C. chinensis from China, Japan and Korea = misidentification of C. jukyungi; C. pyricola and C. pyrisuga from East Asia = misidentification of C. jukyungi and C. burckhardti, respectively; C. pyricola from Iran = misidentification of C. bidens, C. pyri and Cacopsylla sp.) are also corrected. There is no evidence for the presence of European pear psyllid species in East Asia.
Collapse
Affiliation(s)
- G Cho
- Department of Agricultural Biotechnology, Insect Biosystematics Laboratory, Research Institute of Agriculture and Life Science, Seoul National University, Seoul151-921, Korea
| | - I Malenovský
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37Brno, Czech Republic
| | - D Burckhardt
- Naturhistorisches Museum, Augustinergasse 2, 4001Basel, Switzerland
| | - H Inoue
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Akitsu, Higashihiroshima, Hiroshima739-2494, Japan
| | - S Lee
- Department of Agricultural Biotechnology, Insect Biosystematics Laboratory, Research Institute of Agriculture and Life Science, Seoul National University, Seoul151-921, Korea
| |
Collapse
|
16
|
Gariboldi MC, Inserra PIF, Lucero S, Failla M, Perez SI, Vitullo AD. Unexpected low genetic variation in the South American hystricognath rodent Lagostomus maximus (Rodentia: Chinchillidae). PLoS One 2019; 14:e0221559. [PMID: 31513588 PMCID: PMC6742371 DOI: 10.1371/journal.pone.0221559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/09/2019] [Indexed: 11/23/2022] Open
Abstract
The South American plains vizcacha, Lagostomus maximus inhabits primarily the Pampean and adjoining Espinal, Monte and Chaquenean regions of Argentina. In order to study the population genetic structure of L. maximus, a fragment of 560 bp of the mitochondrial DNA hypervariable region 1from 90 individuals collected from the 3 subspecies and 8 groups along Argentina was amplified and analyzed. We found 9 haplotypes. The haplotype network did not show an apparent phylogeographical signal. Although low levels of genetic variation were found in all the subspecies and groups analyzed, a radiation of L. maximus would have occurred from the North and Center of the Pampean region toward the rest of its geographic range in Argentina. Low levels of genetic diversity, the existence of a single genetically distinct population in Argentina and changes of its effective size indicate that metapopulation processes and changes in human population dynamics during the late-Holocene were important factors shaping the population genetic structure of L. maximus in Argentina.
Collapse
Affiliation(s)
- María Constanza Gariboldi
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - Pablo Ignacio Felipe Inserra
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sergio Lucero
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- División de Mastozoología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Sergio Iván Perez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de la Plata, Buenos Aires, Argentina
| | - Alfredo Daniel Vitullo
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
17
|
Park JS, Husseneder C, Schlub RL. Morphological and Molecular Species Identification of Termites Attacking Ironwood Trees, Casuarina equisetifolia (Fagales: Casuarinaceae), in Guam. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:1902-1911. [PMID: 31162600 DOI: 10.1093/jee/toz097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Ironwood trees (Casuarina equisetifolia subsp. equisetifolia L.) are ecologically and economically important trees in tropical and subtropical regions of the Indo-Pacific. Ironwood is one of the dominant tree species in Guam, but since 2002, this tree has been declining dramatically. A previous study showed that numerous sick or dead trees were under termite attack. However, the species of termites were not identified. As a first step to investigate causal relationships between termites and ironwood tree death, we assigned termites collected from ironwood trees to species using a combination of morphological characters and DNA barcoding of the 12S, 16S, COI, COII, and ITS2 regions. Based on morphology and comparisons to reference sequences in NCBI GenBank, the most likely species assignments were Nasutitermes takasagoensis (Nawa) (Blattodea: Termitidae) found to infest 45 trees, followed by Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) (2 trees), Microcerotermes crassus Snyder (Blattodea: Termitidae) (2 trees), and an additional unidentified Microcerotermes species (1 tree) with no close sequence match to identified species in NCBI GenBank. However, taxonomic revisions and broader representation of DNA markers of well-curated specimen in public databases are clearly needed, especially for the N. takasagoensis species complex.
Collapse
Affiliation(s)
- Jong-Seok Park
- S1-5 203a, Chungbuk National University, Seowon-gu, Chengju, Chungbuk, South Korea
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Claudia Husseneder
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Robert L Schlub
- University of Guam, Cooperative Extension Service, Mangilao, Guam
| |
Collapse
|
18
|
Hinojosa JC, Koubínová D, Szenteczki MA, Pitteloud C, Dincă V, Alvarez N, Vila R. A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol 2019; 28:3857-3868. [PMID: 31233646 DOI: 10.1111/mec.15153] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.
Collapse
Affiliation(s)
| | - Darina Koubínová
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Mark A Szenteczki
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Camille Pitteloud
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETHZ, Zürich, Switzerland
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nadir Alvarez
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| |
Collapse
|
19
|
Powell C, Caleca V, Sinno M, van Staden M, van Noort S, Rhode C, Allsopp E, van Asch B. Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa. Genome 2019; 62:183-199. [DOI: 10.1139/gen-2018-0068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Braconidae and six species of Chalcidoidea were identified, and DNA barcoding methodologies were used to investigate conspecificity among individuals, based on randomly selected representative specimens. Morphological identifications were congruent with DNA data, as NJ and ML trees correctly placed the sequences for each species either at the genus or species level, depending on the available taxa coverage, and genetic distances strongly supported conspecificity. No clear evidence of cryptic diversity was found. Overall seed infestation and parasitism rates were higher in wild olives compared to cultivated olives, and highest for Eupelmus spermophilus and Utetes africanus. These results can be used for early DNA-based detection of wasp larvae in olives and to further investigate the biology and ecology of these species.
Collapse
Affiliation(s)
- Chante Powell
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Virgilio Caleca
- Department of Agricultural and Forestry Sciences, University of Palermo, Italy
| | - Martina Sinno
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Michaela van Staden
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Simon van Noort
- Division of Entomology, Department of Natural History, Iziko South African Museum, Cape Town, South Africa
| | - Clint Rhode
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| | - Elleunorah Allsopp
- Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch, South Africa
| | - Barbara van Asch
- Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa
| |
Collapse
|
20
|
Molecular Analysis of Forensically Important Blow Flies in Thailand. INSECTS 2018; 9:insects9040159. [PMID: 30413082 PMCID: PMC6315464 DOI: 10.3390/insects9040159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 11/17/2022]
Abstract
Blow flies are the first insect group to colonize on a dead body and thus correct species identification is a crucial step in forensic investigations for estimating the minimum postmortem interval, as developmental times are species-specific. Due to the difficulty of traditional morphology-based identification such as the morphological similarity of closely related species and uncovered taxonomic keys for all developmental stages, DNA-based identification has been increasing in interest, especially in high biodiversity areas such as Thailand. In this study, the effectiveness of long mitochondrial cytochrome c oxidase subunit I and II (COI and COII) sequences (1247 and 635 bp, respectively) in identifying 16 species of forensically relevant blow flies in Thailand (Chrysomya bezziana, Chrysomya chani, Chrysomya megacephala, Chrysomya nigripes, Chrysomya pinguis, Chrysomya rufifacies, Chrysomya thanomthini, Chrysomya villeneuvi, Lucilia cuprina, Lucilia papuensis, Lucilia porphyrina, Lucilia sinensis, Hemipyrellia ligurriens, Hemipyrellia pulchra, Hypopygiopsis infumata, and Hypopygiopsis tumrasvini) was assessed using distance-based (Kimura two-parameter distances based on Best Match, Best Close Match, and All Species Barcodes criteria) and tree-based (grouping taxa by sequence similarity in the neighbor-joining tree) methods. Analyses of the obtained sequence data demonstrated that COI and COII genes were effective markers for accurate species identification of the Thai blow flies. This study has not only demonstrated the genetic diversity of Thai blow flies, but also provided a reliable DNA reference database for further use in forensic entomology within the country and other regions where these species exist.
Collapse
|
21
|
Kaya S, Çıplak B. Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences. Heliyon 2018; 4:e00929. [PMID: 30519651 PMCID: PMC6260432 DOI: 10.1016/j.heliyon.2018.e00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/06/2018] [Accepted: 11/08/2018] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA has been the preferential genome biodiversity studies. However, several factors contribute to its inadequacy. Numts constitute one of the main complications that prevent obtaining orthologous mitochondrial sequences. Orthoptera have been a model group in numt studies because of their huge genome size. In this study we aimed to; (i) test efficiency of standard PCR protocol in producing orthologous sequences of cytochrome C oxidase, (ii) study presence/absence of numts in several unstudied Orthoptera species, (iii) test if there is a threshold between the length of mtDNA targeted for amplification and possibility of encountering numts, and (iv) estimate reliability of the sequences in databases in light of these findings. For these aims we studied 38 species of Orthoptera representing different sublineages and genome sizes. DNA extracted from each sample was used to amplify five different fragments of COI region by standard PCR protocol. Sequenced PCR amplicons were checked for numt possibility by several different numt criteria. No sequences without numt signs were obtained for the first fragment. The number of samples with numt signs for the other four fragments differed between the suborders Ensifera and Caelifera. The percentage of samples with numt signs was higher in Caelifera than Ensifera for all fragments. The numt percentage considerably decreased for the longest two fragments. Numts are more prevalent in families with larger genome size. We arrived at the following conclusions: (i) numts are common in all members of Orthoptera, but, their prevalence differs among intra-lineages, especially more prevalent in Caelifera, (ii) there seems a correlation between numt rate and genome size, (iii) there is no threshold to avoid numt co-amplification, but, a 1,000 bp length may be a threshold for Ensifera, (iv) Folmer region of COI doesn't seem an appropriate marker for animal barcoding. Additionally, a phylogenetic tree produced from the numt sequences of fragment four detected in genus Anterastes suggested a paleonumt gained in generic ancestor a 3.5-4 times slower divergence rate for numt sequences.
Collapse
Affiliation(s)
- Sarp Kaya
- Mehmet Akif Ersoy Üniversitesi, Burdur Vocational School of Healt Services, Burdur, Turkey
| | - Battal Çıplak
- Department of Biology, Faculty of Science, Akdeniz University, 07058, Antalya, Turkey
| |
Collapse
|
22
|
Ma C, Li J. Comparative analysis of mitochondrial genomes of the superfamily Grylloidea (Insecta, Orthoptera) reveals phylogenetic distribution of gene rearrangements. Int J Biol Macromol 2018; 120:1048-1054. [PMID: 30172811 DOI: 10.1016/j.ijbiomac.2018.08.181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/20/2018] [Accepted: 08/30/2018] [Indexed: 12/27/2022]
Abstract
To further characterize mitochondrial genome (mitogenome) features of the superfamily Grylloidea (Insecta, Orthoptera), mitogenomes of Cacoplistes rogenhoferi and Meloimorpha japonica representing the family Mogoplistidae and three Ornebius species of Phalangopsidae were sequenced. A repeat-containing control region (CR) and 37 genes were present in these mitogenomes. Unusual start codons (TCG, CCG, and CTG) of cox1 and, in Ornebius, a partial stop codon (T) of nad1 followed by a 15-17-bp intergenic spacer were proposed based on transcript information and sequence alignments. The mitogenome-based phylogenetic trees suggest strongly the familial relationships as (((Phalangopsidae + Gryllidae) + Trigonidiidae) + Mogoplistidae). The exclusive occurrence of the trnE-trnS1-trnN rearrangement in Phalangopsidae, Gryllidae, and Trigonidiidae is suggestive of its appearance in the common ancestor of these families after the separation of Mogoplistidae. The trnV transposition in O. bimaculatus and formerly sequenced Trigonidium sjostedti (Trigonidiidae) indicates a potential consequence of parallel evolution. This study offers novel insights into mitogenome evolution, especially gene rearrangements, of Grylloidea.
Collapse
Affiliation(s)
- Chuan Ma
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| |
Collapse
|
23
|
Karthika P, Vadivalagan C, Thirumurugan D, Kumar RR, Murugan K, Canale A, Benelli G. DNA barcoding of five Japanese encephalitis mosquito vectors (Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui). Acta Trop 2018; 183:84-91. [PMID: 29625090 DOI: 10.1016/j.actatropica.2018.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/17/2018] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
Abstract
Culex mosquitoes can act as vectors of several important diseases, including Japanese encephalitis, West Nile virus, St. Louis encephalitis and equine encephalitis. Besides the neurological sequelae caused in humans, Japanese encephalitis can lead to abortion in sows and encephalitis in horses. Effective vector control and early diagnosis, along with continuous serosurveillance in animals, are crucial to fight this arboviral disease. However, the success of vector control operations is linked with the fast and reliable identification of targeted species, and knowledge about their biology and ecology. Since the DNA barcoding of Culex vectors of Japanese encephalitis is scarcely explored, here we evaluated the efficacy of this tool to identify and analyze the variations among five overlooked Culex vectors of Japanese encephalitis, Culex fuscocephala, Culex gelidus, Culex tritaeniorhynchus, Culex pseudovishnui and Culex vishnui, relying to the analysis of mitochondrial CO1 gene. Variations in their base pair range were elucidated by the entropy Hx plot. The differences among individual conspecifics and on base pair range across the same were studied. The C (501-750 bp) region showed a moderate variation among all the selected species. C. tritaeniorhynchus exhibited the highest variation in all the ranges. The observed genetic divergence was partially non-discriminatory. i.e., the overall intra- and inter nucleotide divergence was 0.0920 (0.92%) and 0.125 (1.25%), respectively. However, 10X rule fits accurately intraspecies divergence <3% for the five selected Culex species. The analysis of individual scatter plots showed threshold values (10X) of 0.008 (0.08%), 0.005 (0.05%), 0.123 (1.23%), 0.033 (0.33%) and 0.019 (0.19%) for C. fuscocephala, C. gelidus, C. tritaeniorhynchus, C. pseudovishnui and C. vishnui, respectively. The C. tritaeniorhynchus haplotypes KU497604, KU497603, AB690847 and AB690854 exhibited the highest divergence range, i.e., from 0.465 -0.546. Comparatively, the intra-divergence among the other haplotypes of C. tritaeniorhynchus ranged from 0-0.056. The maximum parsimony tree was formed by distinctive conspecific clusters with appreciable branch values illustrating their close congruence and extensive genetic deviations. Overall, this study adds valuable knowledge to the molecular biology and systematics of five overlooked mosquito species acting as major vectors of Japanese encephalitis in Asian countries.
Collapse
Affiliation(s)
- Pushparaj Karthika
- Department of Zoology, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore 641 043, Tamil Nadu, India
| | - Chithravel Vadivalagan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India; Entomology Laboratory, Department of Zoology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India.
| | - Durairaj Thirumurugan
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Rangaswamy Ravi Kumar
- Centre for Medical Entomology and Vector Control, National Center for Disease Control, M/o Health and Family Welfare, Govt. of India, 22-Shamnath Marg, Delhi, 110054, India
| | - Kadarkarai Murugan
- Entomology Laboratory, Department of Zoology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India; Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632 115, Tamil Nadu, India
| | - Angelo Canale
- Department of Agriculture, Food and Environment, University of Pisa, via del Borghetto 80, 56124 Pisa, Italy
| | - Giovanni Benelli
- Department of Agriculture, Food and Environment, University of Pisa, via del Borghetto 80, 56124 Pisa, Italy; The BioRobotics Institute, Sant'Anna School of Advanced Studies, viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy.
| |
Collapse
|
24
|
Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
Collapse
Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| |
Collapse
|
25
|
Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 2018; 6:e4577. [PMID: 29736329 PMCID: PMC5936072 DOI: 10.7717/peerj.4577] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
Collapse
Affiliation(s)
- Nadine Havemann
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Lars Hendrich
- Sektion Insecta varia, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Jèrôme Morinière
- Taxonomic coordinator-German Barcode of Life (GBOL), SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Rolf Niedringhaus
- Department of Biology, Earth and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Peter Schäfer
- B.U.G.S. (Biologische Umwelt-Gutachten Schäfer), Telgte, North-Rhine Westphalia, Germany
| | - Michael J Raupach
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| |
Collapse
|
26
|
Ivanov V, Lee KM, Mutanen M. Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression. Mol Ecol 2018; 27:1681-1695. [PMID: 29575366 DOI: 10.1111/mec.14564] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 02/23/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022]
Abstract
Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.
Collapse
Affiliation(s)
- Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| |
Collapse
|
27
|
Morinière J, Hendrich L, Balke M, Beermann AJ, König T, Hess M, Koch S, Müller R, Leese F, Hebert PDN, Hausmann A, Schubart CD, Haszprunar G. A DNA barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera). Mol Ecol Resour 2017; 17:1293-1307. [DOI: 10.1111/1755-0998.12683] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Jérôme Morinière
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Lars Hendrich
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Michael Balke
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research; University of Duisburg-Essen; Essen Germany
| | - Tobias König
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
| | - Monika Hess
- Büro H2 Ökologische Gutachten, Hess & Heckes GbR; München Germany
| | | | | | - Florian Leese
- Aquatic Ecosystem Research; University of Duisburg-Essen; Essen Germany
- Center for Water and Environmental Research (ZWU); University of Duisburg-Essen; Essen Germany
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics; University of Guelph; Guelph ON Canada
| | - Axel Hausmann
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
| | | | - Gerhard Haszprunar
- Bavarian State Collection of Zoology (SNSB - ZSM); München Germany
- Department Biology II and GeoBioCenter; Ludwig-Maximilians-University; München Germany
| |
Collapse
|
28
|
Augot D, Mathieu B, Hadj-Henni L, Barriel V, Zapata Mena S, Smolis S, Slama D, Randrianambinintsoa FJ, Trueba G, Kaltenbach M, Rahola N, Depaquit J. Molecular phylogeny of 42 species of Culicoides (Diptera, Ceratopogonidae) from three continents. ACTA ACUST UNITED AC 2017. [PMID: 28643630 PMCID: PMC5482051 DOI: 10.1051/parasite/2017020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The genus Culicoides includes vectors of important animal diseases such as bluetongue and Schmallenberg virus (BTV and SBV). This genus includes 1300 species classified in 32 subgenera and 38 unclassified species. However, the phylogenetic relationships between different subgenera of Culicoides have never been studied. Phylogenetic analyses of 42 species belonging to 12 subgenera and 8 ungrouped species of genus Culicoides from Ecuador, France, Gabon, Madagascar and Tunisia were carried out using two molecular markers (28S rDNA D1 and D2 domains and COI mtDNA). Sequences were subjected to non-probabilistic (maximum parsimony) and probabilistic (Bayesian inference (BI)) approaches. The subgenera Monoculicoides, Culicoides, Haematomyidium, Hoffmania, Remmia and Avaritia (including the main vectors of bluetongue disease) were monophyletic, whereas the subgenus Oecacta was paraphyletic. Our study validates the subgenus Remmia (= Schultzei group) as a valid subgenus, outside of the subgenus Oecacta. In Europe, Culicoides obsoletus, Culicoides scoticus and Culicoides chiopterus should be part of the Obsoletus complex whereas Culicoides dewulfi should be excluded from this complex. Our study suggests that the current Culicoides classification needs to be revisited with modern tools.
Collapse
Affiliation(s)
- Denis Augot
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Bruno Mathieu
- Institut de Parasitologie et de Pathologie Tropicale de Strasbourg, Université de Strasbourg, Faculté de Médecine, 3 rue Koeberlé, EA7292, Strasbourg 67000, France
| | - Leila Hadj-Henni
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Véronique Barriel
- Muséum National d'Histoire Naturelle, CR2P-UMR 7207 CNRS, MNHN, UPMC, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Sonia Zapata Mena
- Instituto de Microbiologia, Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito, Cumbayá, EC170157 Quito, Pichincha, Ecuador
| | - Sylvia Smolis
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| | - Darine Slama
- Laboratory of Medical and Molecular Parasitology-Mycology, Faculty of Pharmacy, University of Monastir, 99UR/08-05, 5000 Monastir, Tunisia
| | | | - Gabriel Trueba
- Instituto de Microbiologia, Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito, Cumbayá, EC170157 Quito, Pichincha, Ecuador
| | - Matthieu Kaltenbach
- Laboratoire de Pharmacologie, Université de Reims Champagne-Ardenne, UFR Pharmacie, 51 rue Cognacq-Jay, 51100 Reims, France
| | - Nil Rahola
- Unité MIVEGEC, UMR 224-5290 IRD-CNRS-UM, Centre IRD de Montpellier, BP 64501, 911 avenue Agropolis, 34394 Montpellier, France - Centre International de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon
| | - Jérôme Depaquit
- USC Vecpar, ANSES-LSA, Université de Reims Champagne-Ardenne, SFR Cap Santé, Faculté de Pharmacie, 51 rue Cognacq-Jay, EA 4688, Reims 51096, France
| |
Collapse
|
29
|
Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G. DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Mol Ecol Resour 2016; 17:1037-1053. [PMID: 27863033 DOI: 10.1111/1755-0998.12638] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022]
Abstract
We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life and Swiss Barcode of Life. Our data set includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. Ninety-three of these 122 species (76.2%, including all Ensifera) can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.
Collapse
Affiliation(s)
- O Hawlitschek
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37, 08003, Barcelona, Spain
| | - J Morinière
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - G U C Lehmann
- Department of Biology, Behavioural Physiology, Humboldt University Berlin, Invalidenstr. 43, 10115, Berlin, Germany
| | - A W Lehmann
- Orthoptera Working Group Brandenburg and Berlin, Friedensallee 37, 14532, Stahnsdorf, Germany
| | - M Kropf
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), Gregor Mendel-Str. 33, 1180, Vienna, Austria
| | - A Dunz
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - F Glaw
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - M Detcharoen
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - S Schmidt
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - A Hausmann
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany
| | - N U Szucsich
- 3rd Zoological Dep., Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - S A Caetano-Wyler
- Université de Genève, Département de Génétique et Evolution, Quai Ernest Ansermet 30, 1211, Geneva 4, Switzerland
| | - G Haszprunar
- Zoologische Staatssammlung München (SNSB-ZSM), Münchhausenstr. 21, 81247, München, Germany.,Department Biology II and GeoBio-Center of Ludwig-Maximilians-Universität München, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| |
Collapse
|
30
|
Verovnik R, Wiemers M. Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes. Zookeys 2016; 600:131-54. [PMID: 27408604 PMCID: PMC4926685 DOI: 10.3897/zookeys.600.7798] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/09/2016] [Indexed: 11/12/2022] Open
Abstract
The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the 'Mamurra' species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution.
Collapse
Affiliation(s)
- Rudi Verovnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjev 101, Ljubljana, Slovenia
| | - Martin Wiemers
- UFZ – Helmholtz-Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120 Halle, Germany
| |
Collapse
|
31
|
Aguilar-Velasco RG, Poteaux C, Meza-Lázaro R, Lachaud JP, Dubovikoff D, Zaldívar-Riverón A. Uncovering species boundaries in the Neotropical ant complexEctatomma ruidum(Ectatomminae) under the presence of nuclear mitochondrial paralogues. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12407] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Reina Gabriela Aguilar-Velasco
- Colección Nacional de Insectos; Instituto de Biología; Universidad Nacional Autónoma de México; 3er. circuito exterior s/n, Cd. Universitaria Copilco Coyoacán A. P. 70-233, C. P. 04510 Ciudad de México México
| | - Chantal Poteaux
- Laboratoire d’Éthologie Expérimentale et Comparée; EA 4443, Sorbonne Paris Cité 99 avenue J.-B. Clément 93430 Villetaneuse France
| | - Rubi Meza-Lázaro
- Colección Nacional de Insectos; Instituto de Biología; Universidad Nacional Autónoma de México; 3er. circuito exterior s/n, Cd. Universitaria Copilco Coyoacán A. P. 70-233, C. P. 04510 Ciudad de México México
| | - Jean-Paul Lachaud
- Centre de Recherches sur la Cognition Animale; CNRS-UMR 5169; Université de Toulouse UPS; Bât. IVR3, 118 route de Narbonne 31062 Toulouse Cedex 09 France
- Depto. de Conservación de la Biodiversidad; El Colegio de la Frontera Sur; Avenida Centenario Km. 5.5, AP 424 77074 Chetumal Quintana Roo México
| | - Dmitry Dubovikoff
- Department of Applied Ecology; Faculty of Biology; Saint Petersburg State University; 16th line of Vasilievsky Island, 29 St. Petersburg 199178 Russia
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos; Instituto de Biología; Universidad Nacional Autónoma de México; 3er. circuito exterior s/n, Cd. Universitaria Copilco Coyoacán A. P. 70-233, C. P. 04510 Ciudad de México México
| |
Collapse
|
32
|
Song H, Moulton MJ, Whiting MF. Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta). PLoS One 2014; 9:e110508. [PMID: 25333882 PMCID: PMC4204883 DOI: 10.1371/journal.pone.0110508] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 02/06/2023] Open
Abstract
Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.
Collapse
Affiliation(s)
- Hojun Song
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Matthew J. Moulton
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
| |
Collapse
|
33
|
Hu J, Chen YD, Jiang ZL, Nardi F, Yang TY, Jin J, Zhang ZK. Global haplotype analysis of the whitefly Bemisia tabaci cryptic species Asia I in Asia. ACTA ACUST UNITED AC 2014; 26:232-41. [PMID: 24460161 DOI: 10.3109/19401736.2013.830289] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidiae), is a cryptic species complex comprising a minimum of 24 cryptic species. Some members of this complex are important agricultural pests, causing considerable damage to vegetable as well as ornamental and horticultural crops. Asia I, one of the cryptic species of B. tabaci, is widely distributed in Asia. One hundred and sixty mitochondrial cytochrome oxidase I (COI) sequences from eight countries have been analyzed to investigate the geographic origin and current genetic structure of this cryptic species. Sixty different haplotypes were identified, with levels of genetic distances ranging from 0.001 to 0.021. A sign of possible genetic differentiation emerges from the differential distribution of dominant haplotypes in Indonesia and India compared to China. A possible ancient separation between Asia I in India and Indonesia and secondary contact in China has been hypothesized.
Collapse
Affiliation(s)
- Jian Hu
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
| | | | | | | | | | | | | |
Collapse
|
34
|
Contreras Gutiérrez MA, Vivero RJ, Vélez ID, Porter CH, Uribe S. DNA barcoding for the identification of sand fly species (Diptera, Psychodidae, Phlebotominae) in Colombia. PLoS One 2014; 9:e85496. [PMID: 24454877 PMCID: PMC3893204 DOI: 10.1371/journal.pone.0085496] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/25/2013] [Indexed: 12/03/2022] Open
Abstract
Sand flies include a group of insects that are of medical importance and that vary in geographic distribution, ecology, and pathogen transmission. Approximately 163 species of sand flies have been reported in Colombia. Surveillance of the presence of sand fly species and the actualization of species distribution are important for predicting risks for and monitoring the expansion of diseases which sand flies can transmit. Currently, the identification of phlebotomine sand flies is based on morphological characters. However, morphological identification requires considerable skills and taxonomic expertise. In addition, significant morphological similarity between some species, especially among females, may cause difficulties during the identification process. DNA-based approaches have become increasingly useful and promising tools for estimating sand fly diversity and for ensuring the rapid and accurate identification of species. A partial sequence of the mitochondrial cytochrome oxidase gene subunit I (COI) is currently being used to differentiate species in different animal taxa, including insects, and it is referred as a barcoding sequence. The present study explored the utility of the DNA barcode approach for the identification of phlebotomine sand flies in Colombia. We sequenced 700 bp of the COI gene from 36 species collected from different geographic localities. The COI barcode sequence divergence within a single species was <2% in most cases, whereas this divergence ranged from 9% to 26.6% among different species. These results indicated that the barcoding gene correctly discriminated among the previously morphologically identified species with an efficacy of nearly 100%. Analyses of the generated sequences indicated that the observed species groupings were consistent with the morphological identifications. In conclusion, the barcoding gene was useful for species discrimination in sand flies from Colombia.
Collapse
Affiliation(s)
| | - Rafael J. Vivero
- Program of Study and Control of Tropical Diseases, University of Antioquia, Medellin, Colombia
| | - Iván D. Vélez
- Program of Study and Control of Tropical Diseases, University of Antioquia, Medellin, Colombia
| | - Charles H. Porter
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, United States of America
| | - Sandra Uribe
- Molecular Systematics Group, National University of Colombia, Medellin, Colombia
| |
Collapse
|
35
|
Nuclear rDNA pseudogenes in Chagas disease vectors: Evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North, Central and northern South America. INFECTION GENETICS AND EVOLUTION 2014; 21:134-56. [DOI: 10.1016/j.meegid.2013.10.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 02/04/2023]
|
36
|
Kim SJ, Lee KY, Ju SJ. Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding. Mol Ecol Resour 2013; 13:781-7. [PMID: 23663201 DOI: 10.1111/1755-0998.12119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 11/30/2022]
Abstract
Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.
Collapse
Affiliation(s)
- Se-Joo Kim
- Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science & Technology, Gyeonggi-do, 426-744, Korea
| | | | | |
Collapse
|
37
|
Swisher KD, Munyaneza JE, Crosslin JM. Temporal and spatial analysis of potato psyllid haplotypes in the United States. ENVIRONMENTAL ENTOMOLOGY 2013; 42:381-393. [PMID: 23575030 DOI: 10.1603/en12261] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae), is an economically important pest of potato (Solanum tuberosum L.) crops across the western and central United States, as it is known to cause psyllid yellows disease and to transmit the bacterium that causes zebra chip disease. Recent genotyping of B. cockerelli collected during the 2011 potato growing season identified three psyllid haplotypes within the western and central United States according to their geographical regions: northwestern, western, and central. To understand potato psyllid population dynamics before the year 2011, high resolution melting analysis of the B. cockerelli mitochondrial cytochrome oxidase I-like gene was used to identify the haplotypes of over 450 archived psyllids collected in the western and central United States between the years 1998 and 2010. Results show that the northwestern haplotype was present in Washington State as early as 1998 and has persisted in this region since that time. Likewise, psyllids of the western haplotype have also been present in Washington and Oregon before 2011.
Collapse
Affiliation(s)
- Kylie D Swisher
- United States Department of Agriculture-Agricultural Research Service 24106 North Bunn Rd., Prosser, WA 99350, USA
| | | | | |
Collapse
|