LifeScanner - DNA barcoding for all

On a recent visit to the Biodiversity Institute of Ontario (BIO), home of the Barcode of Life Data Systems (BOLD), I was given a LifeScanner kit. These kits contain four vials, each containing a small amount of ethanol and labeled with a QR code. They are currently intended for use with an iPhone app - no Android support, so I was unable completely to follow the intended workflow. Users can photograph an item for which they would like a DNA-based identification (e.g. an insect, a leaf, some meat or fish served in a restaurant), place a sample in a vial, scan the QR code on the vial with the app, and upload the photo and associated details (including location from the phone GPS). Finally they mail a package containing the four vials to BIO and get notified when they have been sequenced and what identification results.

In my case, I supplied the necessary information separately, but mailed in four moth samples from a few days spent in Florida. The results were interesting.

A Coleophora sp. turned out to be a perfect match (100% similarity with several existing BOLD samples) for Coleophora glaucicolella, which has not been recorded in Moth Photographers Group or BugGuide from Florida.

A gelechiid I had identified as Aristotelia rubidella came back as matching (100% similarity) a large number of specimens registered in BOLD as Aristotelia corallina. This is interesting. The sequence and external appearance and distribution of records clearly indicates that the BOLD specimens are the same as the moth I found, but these do not seem to match A. corallina - see here for all the details.

Then there were two plume moths. One of these is Exelastis pumilio - the BOLD identification came back as Exelastis with the closest match (similarity 97.1%) with E. pumilio. The species identification is in line with the black spots in the termen and dorsum of the forewing.

The other plume moth was one which I examined too casually and initially labeled as Lantanophaga pusillidactylus. The identification came back as Stenoptilodes, which is quite correct - the moth looks exactly like Stenoptilodes taprobanes. Checking this out made me aware than in fact Florida has a second species in the same genus, Stenoptilodes brevipennis, so I can't proceed beyond identification as Stenoptilodes.

Even for these four moths, the LifeScanner kit helped focus identification questions and give confidence around what can be known and what is difficult to confirm.

LifeScanner kits are currently available for sale in the US and Canada from http://kits.lifescanner.net/.

Posted by dhobern dhobern, June 03, 2015 08:15

Observations

Photos / Sounds

What

Dwarf Plume Moth Exelastis pumilio

Observer

dhobern

Date

May 2, 2015 02:20 PM CEST

Description

Hepalastis pumilio Zeller, 1873, to MV light, Kissimmee, Florida, 1/2 May 2015

Photos / Sounds

Square

Observer

dhobern

Date

May 2, 2015 02:07 PM CEST

Description

Stenoptilodes sp., either Stenoptilodes taprobanes (Felder & Rogenhofer, 1875) or Stenoptilodes brevipennis (Zeller, 1874), to MV light, Kissimmee, Florida, 1/2 May 2015

Photos / Sounds

Square

Observer

dhobern

Date

May 1, 2015 05:15 AM CEST

Description

Coleophora sp., to MV light, Kissimmee, Florida, 30 April/1 May 2015

Photos / Sounds

What

Ruby Aristotelia Moth Aristotelia rubidella

Observer

dhobern

Date

May 2, 2015 06:21 AM CEST

Description

Aristotelia rubidella (Clemens, 1860), to MV light, Kissimmee, Florida, 1/2 May 2015

This individual was barcoded:

www.boldsystems.org/index.php/Public_RecordView?processid...

BOLD linked the individual with specimens sharing the same appearance and identical sequences but identified as Aristotelia corallina Walsingham, 1909:

www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=...

However A. corallina, as presented in MPG and BugGuide has a very different appearance from these BOLD specimens:

mothphotographersgroup.msstate.edu/species.php?hodges=1733.1
bugguide.net/node/view/336808

The next closest match in BOLD was to A. rubidella but with lower than 96% similarity:

www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=...

Walsingham's original description of A. corallina is in Biologia Centrali-Americana:

biodiversitylibrary.org/page/593172

1. Aristotelia corallina, sp. n.

Antennae blackish. Palpi with the median joint somewhat expanded outwardly ; cream-whitish, banded externally with a brownish shade ; terminal joint whitish, with two blackish bands. Head rosy cream-colour ; Thorax the same, but with a stronger reddish tinge, the tegulae blackish. Forewings blackish, the dorsum rich rosy reddish, this colour diffused upward along the termen and over the terminal cilia through which runs a somewhat obscurely reduplicated dark shade-line ; terminal cilia blackish, preceded by three small rosy reddish costal spots. Exp. al. 12 mm. Hindwings dark grey ; cilia brownish cinereous. Abdomen brownish cinereous. Legs brownish cinereous, broadly banded with fuscous externally on each joint.

Type ♂ (65760) Mus. Wlsm. (Godm-Salv. GoU.). [PT. (65762) US, Nat. Mus.]

Hab. Mexico: GUERRERO : Amula, 6000 ft., VIII-IX. (H. H. Smith). Three specimens.

The rosy cream of the head, thorax, and dorsum, contrasted with the blackish forewings, renders this species somewhat conspicuous.

This description matches the moths shown in MPG and BugGuide, but not those in BOLD. This suggests that the BOLD specimens represent a presumably undescribed species closely related to A. rubidella and that the identification of these as A. corallina is likely to be incorrect.

Comments

Thumb

That's a fascinating story, Donald! Would be great if the LifeScanner partners with iNat so that the where & when information plus photos is stored here, and later linked to the barcode. Recently someone posted a bunch of butterfly observations from Italy and mentioned that these were collected during an entomological barcoding project. I suggested to create an observation field that contains a link to the barcode once it becomes available (ideally added automatically). There's probably quite a lot of potential bringing seemingly disparate data sets together - along the lines what Roderic Page is proposing in his blog:
http://iphylo.blogspot.com

Posted by jakob about 4 years ago (Flag)
Thumb

Very interesting! Makes me want to put a "?" after much of my identification. How much did it cost to have your 4 samples tested? I could not see a price on their web site.

Posted by allenratzlaff about 4 years ago (Flag)
Thumb

I believe they said a kit currently costs $40 (if I remember correctly), including processing. It is odd that you seem to have to provide all your details before getting that far. Right now, this is probably only generally useful for rich people or those who have a few problem cases they would like to solve.

The trouble is that, compared with the standard 96-cell plates BOLD usually process, it's must all be rather manual at their end - removing samples from tubes, selecting a suitable size piece to sequence, and then running it (presumably as part of an aggregated plate with other samples). Over time, this kind of capability will get cheaper, more accurate (as we have better reference libraries of sequences) and more readily available. I look forward to the day when a reasonably-priced hand-held device allows us to do this in the field.

It's a double-edged sword for amateur natural history though. We can expect vast numbers of our existing species concepts to fragment into clouds of populations with limited connecting gene flow and hence with apparent isolation even where we have seen no separating characters. It opens up countless new opportunities to study biology and evolution, but we're going to find this much less tidy and accessible to amateurs than today.

Posted by dhobern about 4 years ago (Flag)
Thumb

So you have to have an iPhone for this? Or is that why you sent the information along with it?

Posted by codyhough about 4 years ago (Flag)
Thumb

Sadly - at present - iPhone only, which seems a little bit crazy. Having at least an alternative less fancy web interface would allow the same information to get entered by others. The sending along of information separately is not a standardly supported path but they wanted me to test it out.

Posted by dhobern about 4 years ago (Flag)
Thumb

I only just discovered this service. Buying a kit now.

Posted by kueda almost 4 years ago (Flag)
Thumb

Regarding fragmenting of species concepts, maybe it will force people to grapple with the fact that taxonomy cannot completely serve it's function of reflecting evolutionary history AND allowing people to communicate about types of organisms, and that to communicate effectively using names we will have to make some arbitrary decisions about what groups we give names to. IMO, if you need a sequencer to tell two groups apart they should not have separate names, not because the implied biological differences are somehow trivial, but because it makes it too hard to talk about organisms with other people alive today, and (through our writing) with people of the future.

Another question about Lifescanner: do they post the sequence as a new record to BOLD, including primers used?

Posted by kueda almost 4 years ago (Flag)
Thumb

I just got my first two samples back from LifeScanner via the app and I'm not seeing a way to access the sequence data. I did get a cute color coded barcode. Did you get the sequences set to you or was their an online portal where you could get the sequence data back out?

Posted by damontighe almost 4 years ago (Flag)
Thumb

I didn't use the app myself (Android user) and was emailed a link to the data:

http://www.boldsystems.org/index.php/Public_SearchTerms?query=DS-HOBLS

Not sure whether you would have an identifier that may work in place of "DS-HOBLS".

Otherwise, if you have the record identifiers for the individual specimens (processid), you could replace "MOBIL630-15" in the following - that certainly contains the sequence.

http://www.boldsystems.org/index.php/Public_RecordView?processid=MOBIL630-15

Cutting and pasting that sequence into the following form should allow you to get a better feel for how it relates to other sequenced individuals:

http://www.boldsystems.org/index.php/IDS_OpenIdEngine

Posted by dhobern almost 4 years ago (Flag)
Thumb

Thanks for the help. I tried the cut and paste with the two sample identifiers I have
BOLD-4D2
http://www.inaturalist.org/observations/1926899

and

BOLD-EB7
http://www.inaturalist.org/observations/1926901

but they don't seem to bring up any data. Maybe I just need to give it another day or so to get updated into BOLD?

I'll poke Lifescanner direction about how to get access to the sequence.

Posted by damontighe almost 4 years ago (Flag)
Thumb

I suggest you do that - getting access to the actual sequence is clearly critical for most people. You don't want to have to transcribe from the colours (although it seems on BOLD, Red=T, Green=A, Blue=C and Black=G). Good luck.

Posted by dhobern almost 4 years ago (Flag)
Thumb

ha ha, I agree. I'll post on here how I got it so other will know how to get it as well. Thanks for starting this discussion on iNat.

Posted by damontighe almost 4 years ago (Flag)
Thumb

I'm late to the party here--maybe I wasn't following you yet in June when this was posted! @muir just told me about this, then found them on Twitter, then I saw @damontighe was retweeted about it, then saw they linked to this journal post! @kueda did you receive/use your kit yet?

My first thought for this is that I'd LOVE LOVE LOVE to use it to figure out from saliva the identification of the bats that consumed and dispersed the trees I studied in Tanzania for my PhD. Do you think they could do something like that yet? They'd get mostly plant DNA but that would be very different from any animal DNA. Have you seen this, @jakob? Wonder if it would work on poop too from some difficult-to-identify bats.

Posted by carrieseltzer almost 4 years ago (Flag)
Thumb

I also tried out one of these kits (URI below).

http://www.boldsystems.org/index.php/Public_SearchTerms?query=DS-BOWSER

I received no species resolution identifications, but this was because I submitted specimens from difficult groups. In the case of the mycetophilid, there is no corresponding close match on BOLD, but it clearly falls within the Exechiini, both based on the host (Lycoperdon) and the sequence data.

For my purposes of documenting biodiversity of the Kenai National Wildlife Refuge (see iNat place URI below), this is much better than no identification. Presumably, this sequence will soon be assigned to a BOLD BIN, which we can work with given the Refuge's conservation mandate to conserve natural diversity.

https://www.inaturalist.org/places/kenai-national-wildlife-refuge

In-house checklist:

http://www.fws.gov/refuge/Kenai/wildlife_and_habitat/species_list.html

BOLD projects:
http://www.boldsystems.org/index.php/Public_SearchTerms?query=KNWRA

http://www.boldsystems.org/index.php/Public_SearchTerms?query=KNWRE

Regarding BIN's:

http://www.boldsystems.org/index.php/resources/handbook?chapter=2_databases.html&section=bins

I was pleased with the kit and ordered a few more lifescanner kits for my kids to use as part of a homeschool science lesson/project.

Posted by mbowser almost 4 years ago (Flag)
Thumb

@dhobern, what was the process for supplying the necessary information separately? I have limited access to iOS devices as I do not own one. I had used an ipad from my office at work to use the app and submit samples.

Posted by mbowser almost 4 years ago (Flag)
Thumb

@carrieseltzer, yes, I got a kit, used it, and sent it in a month ago. The app is a bit buggy, but I was able to use it to submit my data and receive my IDs (though it constantly re-notifies me that I have new identifications even though I don't). What is so far entirely lacking is a link to my sequences on BOLD, or any information about if or when the data will be available to me, despite numerous emails asking them to provide me with this information. If LifeScanner was designed just to provide people with IDs and not data, I will not be ordering any more kits. And I will be sad.

Posted by kueda almost 4 years ago (Flag)
Thumb

@kueda I'm getting the same glitch about having new data and I hit sync and get nothing. It seems to happen every 3 days. I sent in 2 "challenge" samples; a feather from a grouse and a polychaete and these samples appear to have stalled out at the Sample Received stage (I submitted samples Sept 8). @carrieseltzer I wouldn't feel very confident at this point that they'd be able to get sequence data off of a very challenging sample like saliva or fecal matter at this point. I've emailed a few times asking for access to the raw data or sequence, but have not received anything back. I too am sad, because for the price and ease of use LifeScanner would be a great platform.

Posted by damontighe almost 4 years ago (Flag)
Thumb

Were people ever able to get the DNA on these?

Posted by glmory 4 months ago (Flag)

Add a Comment

Sign In or Sign Up to add comments

Is this inappropriate, spam, or offensive? Add a Flag