Many roads lead to Barcode libraries

Gnaphosa parvula from Churchill, Manitoba

Coincidentally two papers on spider DNA Barcoding have been published around December. they describe two ways to build a reference library for DNA Barcodes which I find very interesting especially as it documents how complementary different approaches can be. A colleague of mine (Rodger Gwiazdowski) is even more fascinated by this as he is particularly interested in the nuts and bolts of library building and we already had a few discussions about the topic. Those were usually fueled by blog posts (either mine or others on new papers). So I guess there will be another one after this contribution. Looking forward to it.

The first study I wanted to introduce is from the colleagues here at BIO:

Arctic ecosystems, especially those near transition zones, are expected to be strongly impacted by climate change. Because it is positioned on the ecotone between tundra and boreal forest, the Churchill area is a strategic locality for the analysis of shifts in faunal composition. This fact has motivated the effort to develop a comprehensive biodiversity inventory for the Churchill region by coupling DNA barcoding with morphological studies. The present study represents one element of this effort; it focuses on analysis of the spider fauna at Churchill.

The Spiders were collected during the few snow-free months in summer over six years. The collections cover a wide range of habitats near Churchill and different methods were used (e.g. hand collecting, pitfall traps, sweep nets). Most specimens were obtained through general collecting efforts by field course students. I actually remember supervising students on two of those trips. More targeted sampling was done by the senior author of the paper (our resident spider man Gerry Blagoev). 

The result of those efforts is the first comprehensive DNA Barcode reference library for the spider fauna of any region. The researchers found 198 species among 2704 specimens that were barcoded, tripling the species count for the Churchill region. Diversity estimates suggest that there might be another 10-20 species awaiting discovery. They failed to detect 22 species reported in earlier work in the region which means that the total Churchill fauna may include nearly 250 species. As collections were made exclusively during the snow-free summer, e.g. vernal species associated with snow edges were unlikely to be sampled. Knowing this will help to focus future efforts to complete this unique library.

When building such a reference library, specimens must either be freshly collected or taken from an existing collection. The latter might not be feasible to fill the gaps in the Churchill library simply because past efforts have been very limited. There is simply not much material available. But what if this is different and species were frequently collected over several decades and deposited in a museum collection such as the Naturalis Biodiversity Center in Leiden?

The second study on my list addressed the question if it we can predict which specimens in a museum collection are likely to yield a successful DNA Barcode sequence. If so, can one optimize resources, wisely select museum specimens to sequence, and plan fresh collections to supplement? The study focused on Dutch spiders.

31 target species were selected. For each of these, a series of increasingly older specimens was selected and sequenced. This was supplemented with freshly collected material representing nearly 150 Dutch spider species. The scientists recorded which specimens successfully produced DNA Barcode sequences and which failed. They also experimented with DNA extraction techniques.

For freshly collected specimens overall, body size is not correlated with sequencing success or failure. But larger species seem to have a longer DNA Barcoding shelf life than smaller species. When using common destructive extraction methods, small spiders yield useful amounts of DNA for only a few years while those with a body length >3 mm can yield a barcode sequence for about 20 years after collection.

Nondestructive extraction techniques can significantly increase the chances of obtaining a barcode sequence. Even small spiders with a body length of 4 mm or less yield DNA Barcode sequences up to an age of about 15 years while larger spiders can yield barcode sequences for a considerably longer time.

Now that is good use for all skeptical curators out there. The success of nondestructive extraction demonstrated here coupled with the need to preserve museum specimens for a variety of research purposes bodes well for museum collections as source material for DNA Barcode libraries.