Speck of Science 2/7/17 – Shark Find in Belize

FIU researcher Demian Chapman and a possible new species of Bonnethead. Source: FIU 

A new species of Bonnethead has been described in Belize by FIU researcher Demian Chapman, thus the scenario of a single widespread species in that region now becomes the story of one or more species with overlapping ranges. The discovery was made after analyzing a snippet of the shark’s genome.

DNA analysis has allowed a much more nuanced perspective on species-level differences beyond the physical characteristics that were once the focus of classically-trained taxonomists. Now scientists are able to classify variance on a genetic level and have refined the technique. Now researchers use a method called DNA barcoding, which needs to examine just a small portion of an animal’s genomic sequence, and is often compared to scanning groceries at your supermarket’s checkout line. Large-scale efforts to catalog and archive these genetic identifiers, such as Barcode of Life, make this data widely accessible.


In addition, this finding was part of a larger initiative, called Finprint, focused on filling in data gaps concerning sharks, fins, and rays – all of which constitute a group of cartilaginous fish known as elasmobranchs. Finprint uses baited remote underwater video (BRUV) as one of their primary tools for studying these creatures. Much of their work appears to be focused on their spatial distribution, identifying regions that could lead to conflict with other uses such as fishing or areas that can be marked as candidates for protection.

 

Discovery from the Otter Side

While this is an amazing story, the urge to not post all the otter jokes is a fight I may lose.

Sherlotter Holmes and John Beaverson

All joking (briefly) aside, the Journal of Systematic Palaeontology just published findings about the otter species Siamogale melilutra as described by Wang et al. Skeletal pieces from three individuals were recovered in western China and used to characterize the ancient otter who outguns the giant river otter of today in size (approximately 50 kg to the giant otter’s 34).

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Giant River Otter. Photo Credit: Ernane Junior, Your Shot, National Geographic

While the specimens had elements reminiscent of both otters and badgers, a few distinctive features allowed researchers to place the animals firmly in subfamily Lutrinae, home to 13 current day otter species. However the paper notes the mixture of characteristics, described in some other genera as well, lead to some interesting questions about the ways in which the two may be related.

On the tail of this amazing find, I share an interesting otter fact which upon learning some years ago, quickly escalated their status in my heart: sea otters have loose folds of skin under their arms they use as pockets for storing food and rocks to use as tools.

I will close with the following video as it would be an otter shame not to:

Speck of Science 1/24/16 – Bees of the Seas

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Many of nature’s means of doing business on land has aquatic parallels. Seagrasses produce seeds and pollen the same way as terrestrial grasses do. However, there are certainly some differences. The pollen grains of seagrasses dwarf their land-based counterparts at almost 50 times larger, and the physics of the water in which pollination occurs certainly follows rules vastly different than those air currents.

Scientists have been postulating for some time about how marine plants get the job done in such a different environment, evident in this 1976 abstract for a submission in Letters to Nature.  Many aquatic plants may reproduce by variations of self-cloning where a sexual partner is not needed to give rise to new individuals. Sea grasses often dabble in a little of both worlds, as both have their evolutionary advantages. Cloning, often referred to more specifically as vegetative propagation in plants, allows underwater flora to quickly take up real estate without expending as many resources.  However, sexual reproduction confers the benefits of genetic variation and adaptability into their populations.

Initially, it was suggested water bore the primary burden of transporting pollen grains from male to female seagrass plants. However, in 2009, a team of researchers from National Autonomous University of Mexico led by  Brigitta van Tussenbroek observed small invertebrate crustaceans visiting turtlegrass (Thalassia testudinum) flowers in a manner that reminded them of terrestrial bees.

To explore whether or not these small creatures had the capacity to truly serve as pollinators, they moved their exploration in the controlled setting of a laboratory. They put turtlegrass and pollinators in tanks sans current, and monitored the movement of pollen grains as well as successful instances of pollination. Both successfully occurred in tanks where crustaceans had been added, but not in tanks where the animals were absent. The research team coined a new term, zoobenthophilous pollination, to describe the marine process they observed.

Seagrasses are vital to human wellbeing in ways similar to oyster reefs, coral reefs, and mangroves, and provide a wealth of services to the environments they thrive in. They are an important food source for manatees, dugongs, turtles, and other creatures. Their root systems stabilizes sea floors. They may serve as nursery grounds for minuscule juvenile fish needing protection from predators. But seagrasses have seen vast decline worldwide, in what could be called a global crisis. Now that we are learning seagrass survival may also have dependence on pollinators, we can only hope we do a better job of conserving these little sea bees than we have their terrestrial counterparts.

Speck of Science 12/1/16 – How Elephants Are Losing Their Tusks

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Small-tusked elephant, source: African Wildlife Foundation

Nature has a fickle way of removing the wheat from the chaff. When organisms are less suited to survival, their chances of lasting long enough to reproduce may be in serious jeopardy. If the deleterious traits are genetic in nature, then there is limited chance they will be handed off to future generations. We call this process natural selection.

One example proving that humans can act as a shaping force similar to mother nature by chiseling the genetic outlook  of a creature is presented in this recent Independent article.The piece describes how African elephants in some regions are being born with smaller tusks or entirely without them, presumably in response to the selective pressure of poaching. While there always have been an elephant here or there born without tusks, the preferential culling of ivory has increased the prevalence of tuskless elephants.

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Photo credit: National Geographic

However, as Snopes suggests (not a source I was expecting to comment on the issue), this particular phenomenon has been noted and written about for years prior. A 1995 paper published in the African Journal of Ecology noted in Queen Elizabeth National Park had jumped from 3-4% up to 9-25%. Collectively in South Luangwa National Park and nearby Lupande Game Management Area, the change was from 10% up to 38% in a 20 year period.

While elephants may be the charismatic mascot for poaching issues, undoubtedly it is an issue that for a multitude of animal species reverberates well beyond just their population size and deeply into the very tapestry of their DNA.

The freeloading lifestyle of fresh water mussels

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Conglutinates of the Ouachita kidneyshell – Chris Barnhart

I study oystery things. In my little myopic scientific snowglobe, I know a few things about shellfish, and I know a few more things about oysters. Then I know the most things about oyster filtration. So there’s still plenty of room for surprise.

This very thing happened this year during a local American Fisheries Society (AFS) meeting where I heard a talk about freshwater mussels. Probably because I always seem to be mucking about in briny water rather than its fresher counterpart, I was rather taken aback learning that many of these species have parasitic larval stages.

After females collect sperm that males eject externally, they fertilize their eggs and stow them in their gills where they develop into a minuscule larval stage called glochidia. These juvenile mussels cannot fully develop however until they somehow reach a host fish. They will encyst themselves into the host’s tissue where they will stay until more fully formed, at which point they will drop off and settle on the river floor. The host fish has graciously and perhaps unknowingly provided the small creature with protection and dispersal.

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The strangest detail of this whole process seems to be the intricate tactics mussels have developed to get their little parasitic spawn into hosts. Some species concentrate their glochidia into structures called conglutinates that they then release into the water. Many resemble prey items attractive to fish like in the video  and picture below:

Others, like mamas in the Lampsilis family keep their little ones closer to them while dangling parts of their mantle tissue to the same affect at the conglutinates described above.

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Lampsilis’ display attracts host fish – Paul L. Freeman, Nature Conservancy

For most species of freshwater mussel, the choice of host fish seems to be relatively specific. In some cases, the species of host has yet to be discovered, which provides fertile ground for research into the topic such as the work that Florida Wildlife Commission’s Blackwater Research and Development Center in Holt, Florida has done.

As with other symbiotic relationships within nature, freshwater mussels are incredibly dependent on the health of their host and the system around them. This has further increased the need for continued research and conservation, and in some instances agencies and institutions have fostered cultivation and propagation efforts.

Speck of Science 11/29/16 – The Bathing of the Tortoise

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A photo of Jonathan dated at around 1886 – Wikimedia Commons

Jonathan, a 184 year old tortoise touted as perhaps the oldest living land animal, seemed a little surprised at times in this video released by the St. Helena government.

The solid scrubbing appeared to be an attempt to renew the vim and vigour of his shell, as Joe Hollins, the vet who did the deed stated: “It is purely for aesthetic reasons.  We want visitors and tourists on the Island to witness the tortoises in their true form, without the obstruction of moss and lichen on their shells.  There is so much interest in Jonathan, St Helena’s most famous animal resident, and we want all who visit him to see him at his best.”

In recent years, Hollins also oversaw an overhaul of Jonathan’s diet, which seems to have increased his overall well being. Sounds like Jonathan has a pretty savvy ally and friend.

 

Speck of Science 8/17/16 – The Greenland Shark abides

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Source: Ocean Treasures Memorial Library

Several news outlets this week have justifiably made a big deal about the Greenland Shark. Recent research suggests these lumbering giants are now the record holder for the longest lived vertebrates we are aware of. This knocks the Bowhead whale from first place, whose age-determination story is fascinating in its own right, bolstered by the presence of an antique eskimo harpoon point.

Often sharks have been aged through examining growth bands present in vertebrae, however Greenland sharks have softer vertebrae that make this challenging. Additionally, due to challenges in reading these rings as sharks age, as well as possible disconnects between growth rate and age, radiocarbon dating has been joining the toolbox for determining fish longevity.  This study used the method with the sharks’ eye lenses.

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These sharks may take up to 150 years to reach sexual maturity, making their population vulnerable if too many individuals are culled before reproducing. They are also bizarrely prone to parasitism by a strangely-elongate copepod (most look more shrimp or lobster-like) that attaches to their eyeball and ultimately causes a march towards blindness. Only 1% of the 1500 sharks in a study concerning infection rates were parasite-free. 85% are afflicted in both eyes. However, due to their reliance on a keen sense of smell, rather than sight, for hunting, it has been suggested that the sharks may actually benefit from the copepod acting as small visible lures that interest nearby prey. However, Dr. George Benz of Middle Tennessee State University with expertise in shark and ray parasites, doubts this theory, instead favoring the idea that Greenland sharks may instead be ambush hunters, taking their targets instead through the element of surprise.

Speck of Science 8/15/16 – Nat Geo Writes About Pooping Comb Jellies

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Still from Ryan M. Bolton 2016 video: https://www.youtube.com/watch?v=weeFO6kLu5o

Lest you think National Geographic is losing their edge, the reason why ctenophores (the phylum to which comb jellies belong) defecating is a big deal is because it was thought this group of creatures had a single opening for both feeding and excreting. University of Miami researcher William Brown debuted videos at the March 2016 Ctenopolooza gathering at the Whitney Lab in St. Augustine (where I’ve done much of my own dissertation field and lab work) that prove otherwise. One of the peculiar videos is featured partway through Nat Geo’s article here. Science writes about the find as well.

One of the most interesting aspects of this find is questions regarding the evolutionary history of gut development. It was thought to be a pretty straight forward pathway from one opening to two. However, because comb jellies evolved before other organisms that still have a single opening, such as sponges, things are looking slightly more interesting. Perhaps ctenophores branched off, and smartly evolved a more complex gut tract independent of these organisms. Or, perhaps some of these single-orificed organisms started with two but lost one over time – similar to the story of some marine mammals that long ago left the sea to become land-dwellers, only to ultimately return again.

 

 

Depth of Field #5 – You’re All Eyespots

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While running to meeting on the University of Florida campus, I looked down and spied this creature on the edge of a concrete walkway. While about the size of one of our local palmetto bugs (a deceivingly quaint name Floridians have bestowed upon one of the local cockroach species), this large docile beetle was far less menacing. I was entranced by its eye spots, and by the discovery of yet another new species (I am a transplant down here and very much dig the constant appearance of novel little beasties).

Due to its unique appearance, it was easy to later discover this insect’s identity – the speckled eastern eyed click beetle, Alaus oculatus. Among its other common names is the eyed elater. Their larval form is known as a wire worm, and due to its carnivorous diet, is often valued by gardeners for its ability to rid vegetation of other less desirable residents.

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Click beetles are members of the family Elateridae and produce their trademark sound when their spine snaps into a groove located on their mesosternum (basically like a bug chest plate). They do this when righting themselves if flipped over, and this snapping action may allow many members of this family to propel themselves away from harm quickly. Additionally, the presence of eyespots in insects are often suggested to be a form of predator deterrence.

 

The Science PhD Experience: My Life is a Series of Home Improvement Stores

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Source: Wikimedia Commons

Never when I signed up for this whole PhD “thing”, did I think that further down along the line I would wander down the aisles of countless formless and faceless Home Depots and Lowes, familiarizing myself with PVC epoxies, pipe cutters, types of quick-pour concrete, and erratically color-coded lengths of rebar. While I am in the very last throes of the natural science component of my dissertation, for stretches within the last year, nary a week would pass without at least one, if not several, trips searching for the miscellanea one needs to make a bare-bones scientific project happen.

My method for estimating oyster filtration rates required the use of sediment traps (see my post about it here) constructed out of buckets and netting. However, the studies that used them prior and upon which I based my design, had employed them in very different settings. My traps had to withstand dynamic ocean conditions, tidal cycles, and the interest of the errant passerby. So thus began the nail-biting process of iterative design. What type of buckets to use to avoid re-suspending sediment? What kind of netting across the mouth? How to affix them to reef? How to weight them so they wouldn’t float away during the first high tide?

Practice run after practice run unfolded as I tried various proto-types. Scuba weights affixed to the mouth of buckets using hose clamps. Testing ways to keep everything in one place using ground anchors, thin lengths of PVC, rebar. Phone calls from nearby good Samaritans who had retrieved my runaway equipment (a PSA if there ever was one for labeling your gear!). A slick (if not utterly lo-fi) double-nested bucket design weighted down with rounds of concrete emerged out the mixture of mishaps and successes.  I then did it all again and tapped into the same recurrent type of process when creating a seawater flow-through system for oyster filtration lab trials.

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All the while, I was running to every hardware store in town, looking for materials of the right shape, weight, and construction for whatever small application I had in mind. Many questions directed towards employees started with “This is going to sound strange, but…”. Eyebrows were raised when I bought 30 of something generally purchased in increments of one or two – “…Doing a lot of yard work this weekend?”  I recall poorly relaying the idea of my experimental sediment traps meant to measure the amount of oyster biodeposits produced during my experiment, and the amusing follow-up question: “Are you trying to keep the oysters from getting away?”

Many questions directed towards employees started with “This is going to sound strange, but…”.

Additionally I had the help of a marine lab machine shop to drill, cut, and sand. I learned how to estimate which equipment I needed for which job. I also had the opportunity to watch those inclined towards clever design and ask plenty of questions. Is there enough water pressure to do that? How do I get the flow to be more laminar? How do I keep this from leaking?

It’s a cultivated skill set, one which rewards those who tinkered with lego and kinex as a kid. Rarely are we told as marine biologists, fisheries scientists, or field ecologists, that we will draw so heavily upon what amounts to being back-of-the-envelope engineers.It’s also a continued argument for the inclusion of the “T” (technology) and the “E” (engineering) part of STEM training that is often desired on the job, but may make scant appearance in a scientist’s formal education.

Most of us instead gain experience through more informal avenues, as the best teacher is often necessity. Also there is no better practice than to constantly build, err, and deconstruct, all while slowly incorporating new fixes and experiencing the fog of confusion out of which comes little sparks of revelation. The act of literally building our science from the ground up is one of ultimate creativity, funneling in threads of right-brain function, and helping us shape solutions in response to whatever demands our research may make of us.

Note: This content has been cross-posted on the blog “From Reef to Rivers: Florida’s Fisheries Science Blog