Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

Hausmann, Axel; Miller, Scott E.; Holloway, J. D.; deWaard, Jeremy R; Pollock, David M.; Prosser, Sean W. J.

doi:10.1139/gen-2015-0197

Cited by 40 publications

(29 citation statements)

References 46 publications

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“…An additional 166 BINs were not even identified to family. It is of paramount importance to DNA barcode the reference collections deposited in both MNHN and NHMUK, using new barcoding technologies (e.g., Zuccon et al 2012) and with a particular focus on types (Hausmann et al 2016) to more precisely estimate the Linnean shortfall (Cardoso et al 2011) in Madagascan moths. Micromoths will be more challenging in this respect because of the need to minimise tissue removal on holotypes, but as an alternative, morphologically linkable non-primary type material is frequently available.…”

Section: Massive 'Linnean Shortfall' Of Micromoths In Madagascarmentioning

confidence: 99%

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

Lopez‐Vaamonde

Sire

Rasmussen

et al. 2019

Genome

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Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island.

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Section: Massive 'Linnean Shortfall' Of Micromoths In Madagascarmentioning

confidence: 99%

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

Lopez‐Vaamonde

Sire

Rasmussen

et al. 2019

Genome

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“…Insect specimens contain valuable genetic information (Wandeler et al, 2007;Tin et al, 2014;Nakahama et al, 2018). Such information is being used in applied entomology, conservation genetics and taxonomy, and reveals the history of the DNA sequences (Tin et al, 2014;Hausmann et al, 2016;Haran et al, 2018;Nakahama et al, 2018). However, there were very few studies on genetic information obtained from dried specimens of insects before the 2000s, because the rapid degradation of DNA in dried specimens of insects renders them unsuitable for genetic analyses (Wandeler et al, 2007;Nakahama & Isagi, 2017).…”

Section: Introductionmentioning

confidence: 99%

Methods for retaining well-preserved DNA with dried specimens of insects

Nakahama¹,

Isagi²,

Itô³

2019

Eur. J. Entomol.

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To prevent degradation, DNA samples are generally preserved in 95-99.5% ethanol or acetone, or in a freezer, or a combination of these (preserved in 95-99.5% ethanol or acetone and stored in a freezer at −20°C to −80°C) because this prevents DNA degradation (Reiss et al., 1995;Quicke et al., 1999;Vink et al., 2005;Nasu et al., 2016). However, the maintenance and space costs associated with immersed or frozen specimens are greater than those associated with dried specimens. The preservation of frozen specimens requires large freezers, which are expensive and may have limited space for specimen preservation and immersed specimens must be regularly checked to ensure that the stock solution has not evaporated. In addition, morphological observations and dissections of 99% ethanol-immersed specimens are diffi cult due to dehydration (Naem et al., 2010). To overcome these problems, we tested whether DNA in the legs of dried specimens of insects can be preserved for a long time. To this end we suspended insects on a pin in 0.2-ml tubes with only the legs immersed in the preservation solution. We also considered the methods used for killing insects, because apart from dragonfl ies Abstract. Dried specimens of insects are increasingly seen as genetic resources. However, genetic analysis of dried specimens of insects is hampered by the deterioration of the DNA. In this study, we developed methods for preparing dried specimens of insects with well-preserved DNA, mainly for PCR-based genetic analysis. First, we compared the effects of either exposure to ethyl acetate vapour for from 10 min to 6 h or by freezing on the fragmentation of DNA in order to determine optimal length of time needed for killing insects using the above methods. Second, we compared the fragmentation of DNA after preservation by drying or immersion of legs in 99.5% ethanol or 99% propylene glycol in 0.2-ml tubes. We assessed degrees of fragmentation of DNA by determining polymerase chain reaction (PCR) success rates with primers for 313-, 710-and 1555-bp fragments using DNA that was collected immediately, and at one, six and 12 months after preparing the specimens. Differing times taken to kill insects did not affect the fragmentation of DNA. In dried specimens, DNA was seriously fragmented after one month, whereas that in legs prepared by immersion in 99.5% ethanol or 99% propylene glycol contained long fragments of DNA (1555 bp~) after 12 months. Propylene glycol was more suitable for preservation than ethanol, because the latter evaporates. Thus, to preserve insect DNA we suggest inserting the pin on which an insect is impaled into the hinged lid of a 0.2-ml tube containing 99% propylene glycol so that when the lid is closed the legs of the insect are preserved in the solution.

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“…Especially important will be thorough comparative studies of male genitalia in the different haplotype groups, given the importance of this character in separating P. mejicanus and P. catullus. In addition, barcodes from the type specimen of P. catullus could potentially provide important baseline data for future taxonomic studies [53,54]. However, the type(s) of P. catullus collected from a locality named 'Indiis' are probably lost [9].…”

Section: Sootywingsmentioning

confidence: 99%

“…Because a COI barcode is not available for the type specimen, it is possible that Plötz [56] may have examined any one of the several cryptic species of Achalarus found in Mexico in his description of A. toxeus in 1882. This uncertainty both highlights the utility of determining barcodes for historical type material [53,54] and the challenges encountered in formally naming new cryptic species revealed by DNA barcoding.…”

Section: Cloudywingsmentioning

confidence: 99%

DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)

Pfeiler

2018

Diversity

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DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology.

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Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

Cited by 40 publications

References 46 publications

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar

Methods for retaining well-preserved DNA with dried specimens of insects

DNA Barcoding and Taxonomic Challenges in Describing New Putative Species: Examples from Sootywing and Cloudywing Butterflies (Lepidoptera: Hesperiidae)

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