DNA Barcoding – Shark Research & Conservation Program (SRC)

By William Evans, SRC Intern

Fishes that rule the world: circumtropical distributions revisited (2015) by Gaither, Bowen, Rocha, and Briggs reviews and updates the list of circumtropical fishes that was published in1960. The term circumtropical is defined by Merriam-Webster dictionary as “surrounding or distributed throughout the tropics”. Circumtropical fishes represent less than 1% of the world’s aquatic vertebrates but are a diverse group that includes common species such as tuna, remoras, sharks and lantern fishes.

“Nurse shark with remoras” by Duncan Wright (User:Sabine’s Sunbird) – en: Image:Nurse shark with remoras.jpg. Licensed under CC BY-SA 3.0 via Wikimedia Commons

A majority of these species are pelagic or bathypelagic. Through recent updates in technology and the availability to access information using resources like Fishbase and the Catalogue of Fishes, the list was updated from the original 107 species from 1960 to 284 species. The scientists were not only able to use online resources but also used DNA sequencing technologies to better comprehend specific genetic lineages, opposed to only using morphology. Although morphology is a tool that most scientists use in the field, there is room for error, especially with species with such close lineages like the great hammerhead and the scalloped hammerhead. By using DNA barcoding, they were able to compile a more accurate list of when a previously listed species was actually more than one.

The researchers searched FishBase from June to December of 2014 to primarily analyze the distribution of the 107 fishes on the original list. Species were removed if they were only found in the southern ocean and subtropical convergences. After using FishBase, they used the Shorefishes of the Tropical Eastern Pacific (EP) and other records. From these searches, species listed as “circumglobal” were removed, as well as species that have no present records in the East Pacific. Google Scholar searches were also used to discover genetic information from using simple searches of the species name, common name, followed with “genetic” or “molecular” and the first 50 results were then analyzed. A search in the Barcode of Life Data System (BOLD) was also used to record sequences and bins for each species for further examination. Many of the species added were bathypelagic (73% of the 196 new species added) and 19 taxa were removed from the original list. Some of the organisms had no or limited genetic data, showing that many species have not been assessed using these current genetic coding tools.

There are some challenges that exist when it comes to creating and editing a list as extensive as this one. One is the availability of information. Cryptic species, ones with difficultly-distinguishable features, can be a problem when doing a biodiversity study. Although some cryptic species, like the scalloped hammerhead, have a plethora of genetic data, others do not. Of the current list, 74% of the species do not have genetic data, which means that the list could be more accurate if more data was available.

“Scalloped hammerhead cocos” by Barry Peters` – 637943300305. Licensed under CC BY 2.0 via Commons

The journal discusses some biological factors that can explain the global distribution of the fishes found on the list. These factors include a vagile adult phase, a long pelagic duration, habitat preference, and old lineages. In addition to biological factors promoting distribution, there are factors that inhibit global distribution. Those mainly include the East Pacific Barrier and the thermal regime. The East Pacific Barrier is defined as a 4000 km to 7000 km region of deep ocean that separates the East Pacific from the Central Pacific which demonstrates the largest divide in circumtropical fauna that inhabit shallower waters. The thermal regime defined as an area off of South Africa with a topographically and hydrologically complex area mainly due to the cooler Benguela Current that moves northward that is deemed lethal to many tropical organisms.

Although the list has been updated to better represent the amount of circumtropical fish species, a majority of the organisms on this list have little to no genetic data, displaying a disconnect in the amount of information that we know. The authors note that as technology advances, more of the ocean is explored, and more studies are done, the list will be modified to thus reflect those changes.

References:

Gaither, M. R., Bowen, B. W., Rocha, L. A. and Briggs, J. C. (2015), Fishes that rule the world: circumtropical distributions revisited. Fish and Fisheries. doi: 10.1111/faf.12136

By Hannah Calich, RJD Graduate Student and Intern

Prior to 2003, when someone wanted to identify a biological specimen they would examine its morphological features (such as the shape, size, or colour of specific body parts). However, identification wasn’t possible with degraded specimens. To combat this, in 2003 Paul Hebert proposed “DNA barcoding” as a way to help identify animals without using morphological measurements (CBOL, 2014).

DNA barcoding uses small pieces of the genetic sequence obtained from a specimen’s DNA sample to determine what species the sample came from. Since the pieces all come from the same area within the DNA sequence, they can be compared to help determine the animal’s species. This concept is similar to how barcodes are used at the grocery store. To the untrained eye all barcodes look very similar, but scanners are able to identify distinct patterns in the barcode and tell the cashier what the product is. To date, over 140,000 animals, 52,000 plants, and 15,000 Fungi and other life forms have had their DNA catalogued for barcoding (CBOL, 2014).

The implications of DNA barcoding extend well beyond simply creating a database. In fact, a recent study by Alfonsi et al. (2013) aimed to investigate the feasibility of using DNA barcoding to help monitor marine mammal biodiversity through strandings along the French Atlantic coast. In the last 10 years over 1,500 marine mammals from 19 different species have stranded along the French Atlantic coast (Figure 1). Unfortunately, 16.8% of the animals (258 animals) could not be identified to the species level due to body decomposition (Figure 2), poor weather conditions, or because the animal was very rare. Identifying these unknown species is important to help researchers determine what species are stranding, where they are stranding, and what (if anything) humans can do to help save these animals.

Locations of stranded marine mammals in Brittany, France (Alfonsi et al., 2013)

Alfonsi et al. (2013) successfully analyzed DNA samples from 92 marine mammals. The data helped confirm that animals were being correctly identified based on morphology when morphological measurements were possible. The data also helped to identify rare species and identify specimens that were too degraded or incomplete to identify based on morphology alone. In addition, Alfonsi et al. (2013) proposed that DNA barcoding could be used to monitor population movements. By combining their findings with the ongoing database, Alfonsi et al. (2013) determined that the two most commonly stranded species were the short-beaked common dolphin (Delphinus delphis) and the gray seal (Halichoerus grypus).

Examples of stranded marine mammals that were identified to the species level using DNA barcoding by Alfonsi et al. (2013). A-Fin Whale (Balaenoptera physalus), B-Risso’s Dolphin (Grampus griseus), C-Short-beaked common dolphin (Delphinus delphis), D-Striped dolphin (Stenella coeruleoalba)

This study was the first to demonstrate that DNA barcoding can be used to monitor marine mammal diversity through strandings data. Additionally, Alfonsi et al. (2013) showed that even when a carcass is severely degraded, good quality DNA samples can still be obtained. While more work is necessary to fine-tune identifying closely related species (e.g., within the Delphininae family), DNA barcoding has the potential to greatly increase the amount of usable data researchers can obtain from marine mammal strandings.

References:

Alfonsi E, Méheust E, Fuchs S, Carpentier F-G, Quillivic Y, Viricel A, Hassani S, Jung J-L (2013) The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (Eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research. ZooKeys 365: 5–24. doi: 10.3897/zookeys.365.5873 Posterior probabilities for species identification determined by the nMDS analysis. doi: 10.3897/zookeys.365.5873.app2

CBOL (2014) What is DNA Barcoding? Received from: http://www.barcodeoflife.org/content/about/what-dna-barcoding

Posts

Fishes that rule the world: circumtropical distributions revisited

DNA Barcoding: What is it and how can it help stranded marine mammals?