Categories
Araba Bioscan

Araba Bioscan SLAM 24 February to 3 March 2023

Categories
Araba Bioscan

Araba Bioscan SLAM 17-24 February 2023

Categories
Araba Bioscan

Araba Bioscan SLAM 10-17 February 2023

Categories
Araba Bioscan

Araba Bioscan SLAM 3-10 February 2023

Categories
Araba Bioscan Lepidoptera

Lepidoptera Barcoding in Araba Bioscan

Background

Araba Bioscan is a project to improve understanding of arthropod (mostly insect) diversity at a single location, a suburban garden in Aranda, ACT close to open natural (dry sclerophyll) areas, including Black Mountain. This is one of the most intensively studied areas for insects in all of Australia, since the Australian National Insect Collection (ANIC) is located beside the Black Mountain reserve.

DNA barcoding

The project collected weekly samples from 23 October 2020 to 29 October 2022 in a Malaise trap. Further samples have been collected since 22 January 2023 using a SLAM trap. The ongoing effort is focused on identifying and documenting some less well-recorded groups, particularly ichneumonid wasps.

Samples from the first year were sent to the Centre for Biodiversity Genomics (CBG) in Guelph, ON, where 8,838 selected insects and other arthropods were extracted and imaged and their DNA barcodes were sequenced. This selection included:

  • 83 spiders (order Araneae)
  • 43 mites (subclass Acari)
  • 428 springtails (class Collembola)
  • 8 millipedes (class Diplopoda)
  • 32 cockroaches/termites (order Blattodea)
  • 274 beetles (order Coleoptera)
  • 4035 flies (order Diptera)
  • 924 true bugs (order Hemiptera)
  • 1573 wasps/bees/ants (order Hymenoptera)
  • 1138 moths/butterflies (order Lepidoptera)
  • 1 mantis (order Mantodea)
  • 64 lacewings (order Neuroptera)
  • 6 crickets/grasshoppers (order Orthoptera)
  • 183 barkflies (order Psocodea)
  • 1 twisted-wing insect (order Strepsiptera)
  • 22 thrips (order Thysanoptera)
  • 1 caddisfly (order Trichoptera)
  • 2 unspecified arthropods and 20 unspecified arachnids

Sequences from 7362 of these specimens matched a BIN (Barcode Index Number, associated with a cluster of DNA barcodes), indicating a high probability that these are the same species or a very close relative. Many of the specimens in these BINs have been identified, so the DNA barcodes provide a tool to assign scientific names to species found at the location.

This post looks at the results for the Lepidoptera specimens sequenced by Guelph. I had already spent many years light-trapping, photographing and identifying insects, and particularly moths, at this site. This includes 2,840 observations of moths and butterflies representing 599 distinct species on iNaturalist (plus many recognisable moths that may be identifiable to genus but have no scientific name).

A team from CBG made several visits to ANIC to sequence reference specimens of most Australian moth species (including many that are unnamed). This means that the barcode library for Lepidoptera is much more complete than for any other group of Australian insects and most forms are associated with at least genus-level identifications.

This makes the Lepidoptera an ideal test case for evaluating the information gain associated with a DNA-based insect survey. Malaise traps are not the preferred tool for sampling Lepidoptera and will not collect many large species which may be very conspicuous at light. On the other hand, they are efficient at collecting smaller insects and have no bias against species that may be drab, inconspicuous and hard to identify base on their external appearance.

The Araba Bioscan barcode data can be explored on the BOLD Australia site. This site holds a snapshot of all data in the Barcode of Life Data Systems (BOLD) that relates to Australian specimens. It allows these specimens to be grouped and viewed by scientific names (based on the identifications provided by submitters) or by BIN clusters. This makes it easier to explore how well identifications align with (mitochondrial) genetic variation.

If BOLD Australia is accessed using the link the supplied above, the taxa and specimens recorded as part of the Araba Bioscan project (specimens with processIDs beginning “GMAEA”) are highlighted in orange.

Of the 1138 Lepidoptera records, 338 are currently identified only as far as the order, 121 are identified only to family, 70 to subfamily, 283 to genus and 326 to species. These specimens span 39 families, 44 subfamilies and 102 genera. Identifications from BOLD include the following 79 species (listed here with the families assigned in BOLD):

  1. Bedellia somnulentella (Bedelliidae, 35 individuals)
  2. Blastobasis tarda (Blastobasidae, 8 individuals)
  3. Tebenna micalis (Choreutidae, 2 individuals)
  4. Cholotis semnostola (Cosmopterigidae, 2 individuals)
  5. Macrobathra ceraunobola (Cosmopterigidae, 1 individual)
  6. Achyra affinitalis (Crambidae, 1 individual)
  7. Uresiphita ornithopteralis (Crambidae, 4 individuals)
  8. Nacoleia rhoeoalis (Crambidae, 18 individuals)
  9. Eutorna tricasis (Depressariidae, 1 individual)
  10. Elachista velox (Elachistidae, 3 individuals)
  11. Anestia semiochrea (Erebidae, 3 individuals)
  12. Asura lydia (Erebidae, 1 individual)
  13. Threnosia heminephes (Erebidae, 1 individual)
  14. Pantydia sparsa (Erebidae, 1 individual)
  15. Pantydia diemeni (Erebidae, 2 individuals)
  16. Sandava xylistis (Erebidae, 1 individual)
  17. Mesophleps crocina (Gelechiidae, 1 individual)
  18. Orthoptila abruptella (Gelechiidae, 1 individual)
  19. Ardozyga stratifera (Gelechiidae, 1 individual)
  20. Ephysteris subdiminutella (Gelechiidae, 1 individual)
  21. Epiphthora thyellias (Gelechiidae, 5 individuals)
  22. Ectropis excursaria (Geometridae, 1 individual)
  23. Lipogya exprimataria (Geometridae, 7 individuals)
  24. Melanodes anthracitaria (Geometridae, 1 individual)
  25. Mnesampela privata (Geometridae, 1 individual)
  26. Phelotis cognata (Geometridae, 27 individuals)
  27. Psilosticha absorpta (Geometridae, 4 individuals)
  28. Zermizinga sinuata (Geometridae, 1 individual)
  29. Poecilasthena thalassias (Geometridae, 5 individuals)
  30. Dialectica scalariella (Gracillariidae, 6 individuals)
  31. Taractrocera dolon (mistaken identification, actually Ocybadistes walkeri, Hesperiidae, 1 individual)
  32. Genduara punctigera (Lasiocampidae, 3 individuals)
  33. Crocanthes prasinopis (Lecithoceridae, 11 individual)
  34. Crocanthes micradelpha (Lecithoceridae, 2 individuals)
  35. Proteuxoa hypochalchis (Noctuidae, 6 individuals)
  36. Chrysodeixis subsidens (Noctuidae, 1 individual)
  37. Acanthodela protophaes (Oecophoridae, 1 individual)
  38. Acantholena hiemalis (Oecophoridae, 1 individual)
  39. Aeolothapsa malacella (Oecophoridae, 1 individual)
  40. Delexocha ochrocausta (Oecophoridae, 1 individual)
  41. Eulechria eriphila (Oecophoridae, 1 individual)
  42. Eusemocosma pruinosa (Oecophoridae, 1 individual)
  43. Garrha rubella (Oecophoridae, 1 individual)
  44. Garrha leucerythra (Oecophoridae, 8 individuals)
  45. Guestia uniformis (Oecophoridae, 1 individual)
  46. Heterozyga coppatias (Oecophoridae, 2 individuals)
  47. Hoplostega ochroma (Oecophoridae, 54 individuals)
  48. Leistomorpha brontoscopa (Oecophoridae, 2 individuals)
  49. Merocroca automima (misspelled as “automina“, Oecophoridae, 1 individual)
  50. Olbonoma triptycha (Oecophoridae, 9 individuals)
  51. Oxythecta lygrosema (Oecophoridae, 1 individual)
  52. Pachyceraia ochromochla (Oecophoridae, 5 individuals)
  53. Philobota cretacea (Oecophoridae, 2 individuals)
  54. Philobota stella (Oecophoridae, 1 individual)
  55. Philobota xiphostola (Oecophoridae, 2 individuals)
  56. Pseudotheta syrtica (Oecophoridae, 1 individual)
  57. Tachystola stenoptera (Oecophoridae, 1 individual)
  58. Telanepsia coprobora (Oecophoridae, 1 individual)
  59. Telanepsia tidbinbilla (Oecophoridae, 2 individuals)
  60. Oenosandra boisduvalii (Oenosandridae, 1 individual)
  61. Belenois java (Pieridae, 1 individual)
  62. Plutella australiana (Plutellidae, 2 individuals)
  63. Prays autocasis (Praydidae, 1 individual)
  64. Spectrotrota fimbrialis (Pyralidae, 10 individuals)
  65. Salma pyrastis (Pyralidae, 1 individual)
  66. Heteromicta pachytera (Pyralidae, 2 individuals)
  67. Crocydopora cinigerella (Pyralidae, 1 individual)
  68. Endotricha pyrosalis (Pyralidae, 2 individuals)
  69. Crocidosema plebejana (Tortricidae, 1 individual)
  70. Strepsicrates macropetana (Tortricidae, 1 individual)
  71. Asthenoptycha hemicryptana (Tortricidae, 1 individual)
  72. Cnephasia orthias (Tortricidae, 2 individuals)
  73. Epiphyas ashworthana (Tortricidae, 3 individuals)
  74. Meritastis pyrosemana (Tortricidae, 5 individuals)
  75. Meritastis polygraphana (Tortricidae, 10 individuals)
  76. Merophyas divulsana (Tortricidae, 4 individuals)
  77. Scieropepla serina (Xyloryctidae, 1 individual)
  78. Eumenodora encrypta (Xyloryctidae, 6 individuals)
  79. Zelleria cynetica (Yponomeutidae, 1 individual)

Reviewing this list identified the issues listed for bullets 31 and 49. These are being corrected in BOLD. The species known to BOLD as Cnephasia orthias Meyrick, 1910 is not a true Cnephasia but belongs to a group for which a new genus needs to be established. Many Australian sources use the name Rupicolana orthias (Meyrick, 1910) (reflecting its placement in an informal “Rupicolana GROUP”, followed apparently by some bad parsing of this name).

56 of these species are ones that I have identified and recorded from light-trapping and other previous activities in the garden. Most of these are common and familiar species. Their detection and recognition from reference reflects the completeness and quality of the reference barcode library for Australian moths.

As expected, most insects collected are smaller moths, with a large proportion of Gelechioidea and especially Oecophorinae (reflecting Australian biodiversity patterns).

There are 23 species that I had not previously identified using non-DNA methods. As the following thumbnails show, many of these are small species without conspicuous markings. Most or all of them are familiar to me as insects that have been difficult or impossible to identify accurately. Around a third of them are moths I confidently identify to genus but which I cannot progress further because it is unclear how to separate some of the named species (often with only late 19th or early 20th century descriptions) or because it is clear that there is massive undescribed or unmapped diversity in the genus.

New species for the site

Nondescript species

I would characterise 12 of these 23 species as ones that lack conspicuous characters: Cholotis semnostola, Mesophleps crocina, Ephysteris subdiminutella, Epiphthora thyellias, Acantholena hiemalis, Guestia uniformis, Pseudotheta syrtica, Telanepsia coprobora, Telanepsia tidbinbilla, Prays autocasis, Scieropepla serina and Eumenodora encrypta. I would not have expected to identify these insects since doing so would require significant specimen preparation and probably dissection, and even then I would not have been confident that identification would be easy. These are all species that must get massively underreported because they are hard to diagnose by classical methods.

Eumenodora encrypta proved to be reasonably common in the garden (six individuals barcoded, even though this is a species with no records currently on iNaturalist). This species is so cryptic that, prior to a 2013 paper by Lauri Kaila, it was only known from the type specimen and its family placement was uncertain. Kaila referenced multiple specimens from Black Mountain and considered it likely that the species is actually common. One of the specimens sequenced in BOLD and now within this BIN (BOLD:AAM4364) is referenced in Kaila 2013, so the identification is assured.

Blastobasis tarda

Most Blastobasis are rather similar in appearance and I have not attempted to identify those in the garden. The BOLD records from this project include eight assigned to Blastobasis tarda and four belonging to a second BIN (BOLD:AAA9854) that lacks any species identification.

Ardozyga stratifera

I believe I would have identified this moth as Ardozyga catarrhacta, which has a very similar appearance and to which I have identified five of my iNaturalist records. Based on the markings along the costa of the forewing, I believe those other records are indeed catarrhacta, but I have probably missed individuals that could have been assigned to stratifera.

Crocanthes prasinopis

This is one of another group of rather similar species. I have usually identified Crocanthes individuals with this general appearance as Crocanthes glycina (which was not recorded among the 13 barcoded individuals of this genus from my garden). Criteria for separating these species remain unclear to me, but a review of my past identifications is in order.

Eulechria eriphila, Garrha rubella and Garrha leucerythra

These three moths are very similar in outward appearance. I knew that Eulechria (a very diverse genus) includes some insects with this general appearance but I would normally assign all these to an unsorted “Garrha” category. I have 71 iNaturalist observations for moths identified to the genus Garrha, but have not generally progressed far with any other than the most well marked species. Since this genus includes so many outwardly similar forms, this has meant that only 25 of 71 were identified to species. DNA barcoding has clarified some of this unresolved diversity, but I need to spend more time before I would feel confident identifying these species by other methods.

Oxythecta lygrosema

Oxythecta are common and reasonably conspicuous moths here, but the genus includes several rather similar species, and I am now convinced that I have consistently misidentified Oxythecta lygrosema as Oxythecta acceptella. The markings on acceptella seem to be much more crisply defined than on lygrosema.

Pachyceraia ochromochla

This identification seems uncertain. Two distinct BINs are placed under this name, both associated with ANIC specimens, but with rather different appearances. My specimens fall into the larger BIN (BOLD:ABX0360) which seems to hold very nondescript moths.

Philobota xiphostola

Philobota is a massive and frequently abundant genus which seems to shuffle a suite of repeated characters to create new species. Several well-marked local species remain undescribed. Even where individuals have been identified to species, there is unhandled diversity – for example, one of the barcoded specimens in this project falls into BIN BOLD:AAV4780, which is identified from ANIC specimens as Philobota stella. I have identified individuals as belonging to this species. However, the specimens identified with this species name in BOLD fall into three different BINs. Whether these merit separation is unclear and would require further investigation.

In the same way, specimens in BOLD for Philobota xiphostola fall into two BINs. One of these, BOLD:ACF1457, is currently only known from three specimens in ANIC that were collected much closer to the NSW coast, but the one holding my specimen, BOLD:AAV4778, includes many more, mainly from around the ACT. It is pleasing to be able to align local Philobota having this appearance with other matching records.

Plutella australiana

Diamondback moths are abundant throughout Australia and a major global pest. Almost everywhere in the world, these can easily be assigned to Plutella xylostella, but Landry & Hebert 2013 recognised a second Australian species, Plutella australiana, only diagnosable via genitalia or DNA.

Since 2013, Australian diamondback moths have generally been identified only to the complex of the two species. The two specimens barcoded in this project both fell into the BIN for australiana. It is gratifying to be able to place a species name at least on these records.

Asthenoptycha hemicryptana

Miscellaneous brown and blotched tortricids are one of my blindspots – I find them very difficult to identify and have not generally bothered with any other than the most clearly marked species. As an indication of the challenge, one of the specimens in BOLD that has been identified as Asthenoptycha hemicryptana falls into BIN BOLD:AAJ9668. This BIN includes specimens associated with five binomials and four placeholder species names, most of them from ANIC.

My specimen falls into BIN BOLD:AAZ9337, with the identification supported by another ANIC specimen.

Based on this confusion, I still feel cautious about identifying this individual any further than Asthenoptycha.

Moths without species identifications

This section includes comments on some of the BINs that do not yet resolve to species identifications.

Dryadaula

Ten small moths matched BIN BOLD:AAM9461 and are identified to belong to the genus Dryadaula. Until recently this was included in the Tineidae, but recent work has established a new family Dryadaulidae. Yang & Li 2021 gives an update on this change and shows some species.

Gracillariidae

BIN BOLD:ABX2205 includes 65 moths. 64 of these are from my garden, with the remaining insect collected by the CBG team a few kilometers away near ANIC. Most of the specimens lack any recognisable features, but it seems to be a mid- to dark-brown gracillariid with a paler head and thorax and ill-defined pale bands across the distal half of the forewings. I suspect that this is a Caloptilia species. Several can be seen in this weekly sample photo from the same week as some of the barcoded individuals.

Perthida

BIN BOLD:AAY1668 includes two individuals that cluster with other specimens of the leafminer genus Perthida (Incurvariidae).

Conclusion

The Australian DNA barcode library still requires massive curation, even for Lepidoptera, which remains the best sampled taxon.

However, even without strategic selection of specimens to barcode a truly representative selection of moths, these Malaise samples demonstrate how DNA-based surveys can complement light-trapping and citizen science observations.

Categories
Araba Bioscan

Araba Bioscan SLAM 27 January to 3 February 2023

Categories
Araba Bioscan

Araba Bioscan 21-28 October 2022

Categories
Araba Bioscan

Araba Bioscan 14-21 October 2022

Categories
Araba Bioscan

Araba Bioscan 7-14 October 2022

Categories
Araba Bioscan

Araba Bioscan 30 September to 7 October 2022