Another year of science closes, giving us pause to review those new species of sharks described in the scientific literature, bringing the total number of known shark species to 512. Perhaps it’s a hollow victory to have so many different species known at a time when sharks populations worldwide are either in decline or in a complete population tailspin. But as taxonomists continue to kick ass and give names, our knowledge of shark evolution, biogeography, and ecology continue to get richer. Meet the new sharks of 2015:

Ginglymostoma unami, the Pacific Nurse Shark
This isn’t really the brand-spankin’ new species you might think, but it has been known for well over a century. The Nurse Shark (Ginglymostoma cirratum) had a disjunct distribution between the Caribbean and Gulf of Mexico and the eastern central Pacific oceans, meaning their range was divided into two separate populations. Like some nooks in the Ozarks, land barriers prevented gene flow, so the populations were both physically and genetically separated by a small spit of land called Central America. This team didn’t use genetic methods to test if the populations were distinct enough to be considered different species, but relied on a meristics, the process of compiling detailed measurements of the shark’s anatomy and comparing these values between the populations.  However, a 2012 paper on populations genetics of G. cirratum showed that the Pacific population was genetically quite unique, and divergent from any of the Atlantic populations. Since these two nurse shark populations had been separated by three million years, a few things can happen, like speciation. Indeed, their analysis showed that these two species are morphologically different enough to warrant giving the Pacific population its own scientific name. This name, G. unami, is an acronym of their alma mater, the Universidad Nacional Autonoma de Mexico.

Moral-Flores, L.F.D., E. Ramirez-Antonio, A. Angulo, and G. Perez-Ponce de Leon. 2015. Ginglymostoma unami sp. nov. (Chondrichthyes: Orectolobiformes: Ginglymostomatidae): una especie nueva de tiburón gata del Pacífico oriental tropical. Revista Mexicana de Biodiversidad 86 (2015) 48-58.

Scyliorhinus ugoi, Dark Speckled Catshark
Way down among Brazilians sharks once swam there in the millions, but overfishing took surely took a hefty toll, yet there are still new shark species to be found. Case in point: a new catshark that had long been swimming along most of the Brazilian coast but had been confused as other known species. Catsharks are a widespread, diverse, and somewhat confusing group of sharks. Differences in color, morphological changes between juveniles & adults, and sexual differences between males & females create difficulties in sorting out just how many species there are. Here, the authors use detailed meristic analysis to extract out a species that had been there all along, but the morphological features that delineate the species had not yet been defined.

SOARES, K.D.A. & GADIG, O.F.B. & GOMES, U.L. 2015. Scyliorhinus ugoi, a new species of catshark from Brazil (Chondrichthyes: Carcharhiniformes: Scyliorhinidae). Zootaxa, 3937 (2): 347-361.

Atelomycterus erdmanni, Spotted-belly Catshark

This sexy beast is one of the more colorful species of catsharks, and is one of several new species discovered from a larger taxonomic mess called the coral catsharks.  Using meristics, genetics, and biogeographical analyses, it turns out that the “coral catshark” represents several species, with this species as the newest. They don’t live in coral, so much as they crawl on and among coral reefs of Indonesia, using their pectoral and pelvic fins like tiny feet and walking like a more limber and agile salamander. Named after Mark Erdmann, a fish taxonomist who collected most of the known specimens, and was rewarded with this li’l shark bearing his name.

Fahmi & White, W.T.  2015. Atelomycterus erdmanni, a new species of catshark (Scyliorhinidae: Carcharhiniformes) from Indonesia. Journal of the Ocean Science Foundation 14: 14-27.

Bythaelurus tenuicephalus, Narrow-head Catshark
2015 also brought us two more catsharks, from the same genus, and both from the depths of the southwestern Indian Ocean. Hailing from the outer continental shelf of Mozambique and Tanzania comes the Narrow-headed catshark. The vast majority of sharks in recent years have been from the more remote pockets of Earth’s oceans, and in particular, from the deep oceans that have barely been explored. This species of Bythaelurus is a “dwarf”, a species that is sexually mature at a much smaller size than most other species in its genus.  The advantage of dwarfism might allow this species to breed at a younger age, thus increasing their overall lifetime reproductive output. Or it could be that being smaller simply means eating smaller prey that larger species of catsharks might miss. This sort of niche-partitioning may explain why there are so many different species of catsharks. The species name tenuicephalus means “narrow head”, a little less imaginative than some names, but descriptive nonetheless.

KASCHNER, C.J. & WEIGMANN, S. & THIEL, R. 2015. Bythaelurus tenuicephalus n. sp., a new deep-water catshark (Carcharhiniformes, Scyliorhinidae) from the western Indian Ocean. Zootaxa, 4013 (1): 120–138.

Bythaelurus naylori, Dusky Snout Catshark
Another year, another catshark on the list.  This species however, has quite an interesting story behind its capture.  Massive trawlers, towing huge nets and pulling up tons of fish aren’t new, but what is new is the trend for these huge vessels to move from depleted fishing grounds in the shallows, and into the relatively untapped fishery resources of the deep sea. In addition to the targeted commercial species that will earn them great sums of money when they return to port, these nets also catch and kill tons of other non-marketable species.  This is what ecologists call ‘by-catch’, but there is a sunny side to such needless destruction.  Commercial vessels are often the first to explore deep-sea zones, well ahead of research cruises that are difficult to fund and even more impossible to sustain over time. If you can get onto one of these factory trawlers, the bounty of the bycatch is yours, and what a paradise this is to shark researchers. Dave Ebert & Paul Clerkin of the Pacific Shark Research Center at Moss Landing Marine Lab got the invite to board one of these vessels as it sailed south from Mauritius, but with a small catch: they had to stay for the entire three month trawling season. If you haven’t ever had the displeasure of sailing the wild waves and howling winds where the Indian Ocean meets the Southern Ocean, then you wouldn’t know that it makes The Deadliest Catch look like a Honolulu harbor cruise. Already hardened by the seas of the Gulf of Alaska, Paul made three of these cruises, collecting more than a dozen new species of skates, rays, sharks, and chimeras that will be published in future years. The species name naylori honors Gavin Naylor of the College of Charleston who, through genetic analysis, is compiling a more complete evolutionary history of extant shark species.

EBERT, D.A. & CLERKIN, P.J. 2015. A new species of deep-sea catshark (Scyliorhinidae: Bythaelurus) from the southwestern Indian Ocean. Journal of the Ocean Science Foundation 15:53-63.

And lastly….
Etmopterus benchleyi, Ninja Lanternshark
If you haven’t already seen this sassy new deepsea shark that went viral late last year, check it out here, and here, and here. That makes six new sharks for 2015, but new species will be discovered and described in 2016, so check back next year.
VÁSQUEZ, V.E. & EBERT, D.A. & LONG, D.J. 2015. Etmopterus benchleyi n. sp., a new lanternshark (Squaliformes: Etmopteridae) from the central eastern Pacific Ocean: Journal of the Ocean Science Foundation; 17: 43-55.

The post Meet the New Sharks of 2015 first appeared on Deep Sea News.

Ken described the project (funded by the US National Science foundation) in a recent e-mail:

We left Punta Arenas Chile Jan 1st, 2013 and arrive into McMurdo Station, Antarctica Feb 7th. The purpose of this cruise is to study genetic patterns of biodiversity in the Bellingshausen, Amundsen and Ross Seas. These are some of the most remote waters on the planet. Given the rapidly changing environment in this region due to climate change, we also want to establish an understanding of where different species currently occur.

You can follow their cruise on Twitter (@Icy_Inverts_AU and  @CMU_Antarctica), and find more information at the websites listed below. Just remember guys, Cabin Fever and/or extended periods of sleeplessness DO NOT MIX WELL with Tweeting.

Blog/web pages:

Icy Inverts 2013 – Shipboard Blog

Icy Inverts 2013 – Project portal at Auburn University

Biology in Antarctica – Project portal at Central Michigan University

YouTube video describing the project:

Auburn University – Icy Inverts 2013 – sorry DSN readers, I couldn’t embed the video here because of the privacy settings :(

The post “Icy Inverts” 2013 Cruise – Scientific Adventures in Antarctic Waters first appeared on Deep Sea News.

A pregnant female whale shark is a juicy mental picture indeed.  I mean, if the whale shark is the largest of all fishes, how gargantuan must be a big ol’ mama, turgid with a teeming horde of spotty little kiddies?  And what must it be like when that next generation finally bursts forth into the world, all 25 dozen of them?  Well, Dr. Schmidt has some slightly disappointing news: they probably don’t erupt quite so dramatically.  That’s because the offspring they studied covered the full gamut of developmental stages from barely-formed, to ready-to-pop little mini-adults. That means the female likely gives birth over an extended period, releasing a few here and few there as each embryo reaches maturity.  This result implies that pregnancy might be a very prolonged affair in whale sharks, and it also raises the possibility of multiple paternity: the idea that different embryos might come from different matings with different males.

That’s where their other discovery comes in.  Using DNA-marker techniques, Dr. Schmidt and colleagues showed that all the embryos they studied had the same genetic father.  How can it be that all embryos have the same dad, but are at all sorts of different stages of development?  Do whale sharks form monogamous pairs that roam the oceans together, pairing regularly?  Probably not.  Rather, it seems likely that female whale sharks mate once then store the sperm internally and use it to fertilise a long sequence of eggs over time, producing a staggered series of offspring.  It’s the reproductive equivalent of sipping, not chugging and is probably an adaptation that serves to maximise the benefit of rare mating encounters and to avoid putting all their, um, “eggs” into one birth basket.

I greatly enjoyed their paper.  It’s an elegant application of genetics and embryology to infer reproductive biology in the absence of direct observation (neither mating nor pupping has ever been seen) and constitutes another great piece of the enigmatic puzzle that is the biology of the world’s largest fish.  If you’re into sharks, I highly recommend it.

Schmidt, J., Chen, C., Sheikh, S., Meekan, M., Norman, B., & Joung, S. (2010). Paternity analysis in a litter of whale shark embryos. Endangered Species Research, 12 (2), 117-124 DOI: 10.3354/esr00300

Joung, S., Chen, C., Clark, E., Uchida, S., & Huang, W. (1996). The whale shark, Rhincodon typus, is a livebearer: 300 embryos found in one “megamamma” supreme Environmental Biology of Fishes, 46 (3), 219-223 DOI: 10.1007/BF00004997

The post Who’s your daddy? first appeared on Deep Sea News.

One of the defining decision points of life: Settle-down and make a living close to the familiar particulars of your birthplace or venture out to get a fresh start and be exposed to additional opportunities and experiences that “somewhere else” could open up.

In addition to vexing angsty young adults on One Tree Hill, the decision to be a close-to-home settler or a long-distance drifter also appears to be encrypted in the genotype of some reef-building corals. And conveniently, the difference appears to be color-coded in coral larvae.

A study published last week in the Proceedings of the Royal Society B. by researchers at the University of Texas at Austin indicates that newborn corals that inherit a particular fluorescent pigment exhibit a selective advantage in traveling further from their home reefs over their counterparts which lack this specific pigment. This has important implications in how coastal resource managers can cope with a future, warmer ocean resulting from climate change. The less likely coral larvae are to settle, the more likely they will disperse far from their reef of origin and find more suitable environmental conditions.

The study focused upon Acropora millepora, a relatively abundant Indo-Pacific stony coral found from Sri Lanka and Thailand to Australia, Tonga, and the Marshall Islands. Adult A. millepora (in the image at the top of this post) are most commonly found in green colonies with orange tips, but can also be bright salmon-pink, blue, green, pale green, bright orange, or pink. A. millepora forms cluster-shaped colonies. Like other stony corals, A. millepora’s visible technicolor hues result from pigments produced by symbiotic algae (dinoflagellates) living within the coral animal tissue. But stony corals can also glow with trippy fluorescing colors of green, red, or blue that are only visible under ultraviolet (UV) wavelengths. Anyone old enough to remember the fuzzy black light posters of the 70’s or techno raves of the 90’s is familiar with fluorescence. [In retrospect, if you remember details from either of these decades, you probably weren’t doing them right.]

Fluorescing proteins (FPs) are responsible for the UV light show on display in adult coral colonies. But coral larvae can also exhibit fluorescent coloration in a variety of color morphs, predominantly bright green and bright red, though the function of this larval fluorescence has been poorly understood.

Dr. Mikhail “Misha” Matz, one of the authors of last week’s published study, and his colleagues decided to investigate whether the presence of FPs offer any clues to eventual life histories of adult coral colonies. Their experimental setup was elegant, with overtones of classical Mendelian inheritance studies. Suffice to say, it required some field collecting of specimens and a goodly amount of fiddling with glassware, microscopes, teeny-tiny instruments, and filtered seawater. I suspect it also involved quite a bit of prancing about the lab sporting fluorescent pigment face-paint whilst bathed in ultraviolet light.

After crossing different color morphs of the Acropora millepora, and exposing the larval offspring to an attractive settlement cue of crushed calcareous red algae–essentially catnip to coral larvae–Matz and his colleagues observed that larvae inheriting redder fluorescent color from their parents were less likely to settle and metamorphose into reef-building polyps than greener larvae.

I wrote Professor Matz last week and asked if he might answer a few follow-up questions. He responded withing 20 minutes of my email with added details. In addressing the practical reef management application of his group’s finding:

“Our finding suggests a link between the color of young corals and their likely dispersal range. If borne out in follow-up studies, this connection could help to evaluate, just by looking at the youngsters’ color in nature, how much a particular reef depends on larvae arriving from other places, versus how well it is able to reseed itself. This has obvious implication for conservation planning (for example, reefs that have lots of immigration would be able to recover faster after disturbances than the predominantly self-seeding reefs, and hence might be better bets for protective measures).”

Prof. Matz doesn’t think the infrastructure necessary in the field for coral reef resource managers to rapidly assay coral spawn as settlers or drifters is prohibitive. Nothing more sophisticated than a flash digital camera capable of macro-photography and some light filters. But before we start placing any camera orders, Prof. Matz has more basic research he’s like to conduct,

“First we must verify that the color-dispersal range connection holds (i) in nature; and (ii) at the individual level. We will hopefully be able to do all the necessary experiments this year.”

And while he and his colleagues definitely sees co-inheritance of fluorescence color and settlement success, the question remains as to why they are co-inherited,

“I expect a functional link (red fluorescence might be participating in sensory functions of the larvae), but it is also possible, at least theoretically, that the “gene for settlement ” and “gene for color” just happen to be next to each other in the genome. Whatever the cause of the co-inheritance, it is definitely real.”

In the case of corals, deciphering these genetic signals involved in settlement of new coral reefs isn’t just an academic puzzle, but potentially the key to seeing reefs through the biggest challenge to their ongoing survival.

C. D. Kenkel, M. R. Traylor, J. Wiedenmann, A. Salih, M. V. Matz (2011). Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress. Proceedings of the Royal Society B: Biological Sciences : 10.1098/rspb.2010.2344

The post Red Means Go: Coral, Color, and Climate Change first appeared on Deep Sea News.

We need to put names on things.

I’m a scientist who has always strived to be integrative—I believe you need to understand all sides of a debate in order to fix the root of the problem.  I’ve tried everything from traditional nematode taxonomy, high-throughput molecular phylogeny, and in-situ hybridization in zebrafish (in my undergrad/Ph.D. era), to nematode genomics, 454 sequencing of whole sediment communities, and transcriptomics in my current postdoc.  I’m also learning computer programming. (Apologies to Carl Zimmer for breaking all the rules in one paragraph.  To my non-scientists, for whom that was all jargon: I have been trained to do research in a LOT of different things).

Compared to the other research I’ve done, nematode taxonomy is hard, back-breaking labor.  You can only look at so many worms per day, and your eyes can only withstand so much beating.  Trust me.  But in spite of these drawbacks,  the only reason we know anything about deep-sea nematodes  (and countless other ‘minor’ phyla) is because of diligent, dedicated taxonomists.

We can’t even do genetics without taxonomy.  My current projects use high-throughput gene sequencing to look at communities of microscopic marine animals living on the seafloor (generating millions of DNA barcodes for many of the neglected phyla that Dr. M mentioned in the article).  We have to match up our DNA sequences with online genetic databases—where someone, somewhere has looked at an individual nematode, tardigrade, or kinorhynch, said “ah, yes, this anatomy means it is Species X” and has then gone on to get a gene sequence for that same animal.   Without a close relative in the database, our DNA sequence from species X will be labelled as having “no match” , and species X will continue to be a name-less, phylum-less enigma.

Yet, taxonomy is an old institution and can be resistant to change.  We know far too much about genetics to deny the utility (and objectivity) of DNA sequences in biodiversity research.  Why aren’t we training integrative taxonomists, who understand morphology but are also adept at sequencing genes?  Why, instead of pushing hard to revolutionize and modernize a powerful field, are scientists watching it die?

Science needs to put names on things—not just because we as humans want to organize life, but because it is critically practical.

In the wake of heartbreaking environmental disasters, public outrage is inevitable.  Companies can get away with murder (the deaths of nameless, undiscovered animals), and wipe their hands clean after paying shockingly lenient fines.

Determining reparations for the Gulf oil spill will be a regulatory process, not an emotional one.  The Natural Resource Damage Assessment (NRDA) process requires a detailed iteration of “damage to ecosystem services” and puts a cost on these perceived damages.  In this case, ignorance really IS bliss (for BP, anyway); in the absence of baseline biological information, the default assumption is that no damage has been done.  If we never knew species were there, we’ll never know that they disappeared.

I believe it is possible to do both high-impact science AND taxonomy within a single project.  With the rapid advance of DNA sequencing technologies, investigating the biodiversity of small, diverse animals is cheaper, faster and more feasible than ever; taxonomy is (and should be) a required complement to these studies.  Integrating historically disparate scientific disciplines will require much resolve, collaboration and enthusiasm amongst scientists.

We are indeed in a biodiversity crisis, but I am ever the optimist.

The post Biodiversity crisis-a call to arms for scientists? first appeared on Deep Sea News.

Editor’s Note: Genomic Repairman is a friend I’ve gotten to know through Twitter (@genrepair). He is a semi-cultured, good-natured graduate student in biomedical sciences who escaped out of the deep south and now focuses on using genetics and biochemistry to elucidate DNA repair in cells. He blogs at Tales From a Genomic Repairman. I asked him to guest post here which he graciously accepted and offered this excellent post on how studying fish has helped us to understand cancer. Enjoy!

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Let me begin with an admission of ignorance, I am not a marine biologist, I do not have a great fundamental understanding of fish or the life aquatic. But I do not let little things like an utter complete lack of knowledge or not having really worked in marine science hold me back from making a post. So my aim is to take a stab at this topic of fish by talking about DNA which I know a great deal about and study how it becomes broken and then how it gets repaired.

Before we get to fish, lets amble on down to another topic, cancer, and more specifically melanoma. Cutaneous malignant melanoma (CMM) is an aggressive form of skin cancer whose incidence seems to be increasing worldwide (1). It is understood that sun exposure is the predominant environmental cause of this cancer but there is likely to be some hereditary disposition for CMM also (2-4).

Cancer research tends to focus on mammalian models for obvious reasons (comparable cell lineage, physiologic similarity to humans, and utility of generating mutants in the case of mice). Non-mammalian models, such as fish, are of great value as well as they are some of the oldest models of cancer and have been proven to be effective (5). Relatively short breeding cycles, large progeny, and low cost of use provide a substantial advantage to their use as models of disease.

Tumor formation in the fish genus Xiphophorus has been well established. Way way back, since after the first great war (that’s WWI to all you that got D’s in history), certain hybrids of the genus (platyfish and swordtails) developed malignant tumors of pigment cells that were classified as melanomas (6). Interestingly enough melanomas from Xiphophorus can be xenografted (a process of transfering tissue between different hosts) onto nude mice and grown. More interestingly, it still maintains fish antigen expression (7). The melanoma-specific cancer gene (e.g. oncogene) locus, known as Tu (as in tumor), is repressed by the R (regulator) locus on another chromosome in fish and selective breeding can be undertaken (8, 9). Through a classical crossing experiment you can develop a variety of pigmented phenotypes by selecting for Tu and breeding R out of the hybrids. This is really dry and if you want more detail I would be more than happy to talk to you about it, but lets face it breeding strategies are quite boring and better left to personal discussions than blog posts.

So what is this Tu? Cloning and genetic disruption experiments revealed that the gene at the Tu locus is EGFR-related and is responsable for melanoma formation (10, 11). The gene Xmrk (Xiphophorus melanoma receptor kinase) arose from a tandem duplication event of Xiphophorus EGFR and was found to be highly expressed (i.e. “turned on”) in transformed pigment cells of certain hybrids (12). So what is Xmrk doing in the cell? Xmrk is working through the classic Ras-Raf-MAPK pathway to stimulate cell proliferation as well as activating STAT5, which promotes anti-apoptotic (apoptosis=cell death) signaling as well as in addition to proliferation.

Enough about Xmrk, what is R? Well we only kind of have an idea and its not too solid. While genetic evidence points to the CDKN2AB gene, a homologue of cyclin-dependant kinase inhibitor p16, to be the candidate tumor suppressor, the functional evidence so far is unclear (8). Therefore this remains an area of intense focus for fish researchers. Similarly further characterization of tumor modifier genes still needs to be sorted out as well. Recently, a new fish melanoma model has been reported in the literature. The Schartl lab used the medaka fish (Oryzias latipes) to create a transgenic Xmrk fish that results in a highly invasive and more metastatic melanoma, which may be more suitable model of human melanoma (13).

Before leaving you guys, lets talk about another possible benefit of using fish as a model of melanoma. Small molecule inhibitor screens are all the rage these days and these fish could be integral in finding chemicals that interfere with different aspects of melanocyte biology: pigmentation, migration, and cell survival. This in vivo testing model involves placing embryos in well plates and treating with specific chemicals in the water, creating a cheap and rapid in vivo testing system for small molecules.

Marine science research is important and can have implications on human health as well. This is but one example how someone studying fish noticed a phenomena that had suitable implications for a human disease. So go study fish, who knows, your research might be helpful in fighting cancer one day. So folks this is where I’m going to stop the car and let you out. I hope this has been informative and not too dry. Once again, my focus is fish, so I may have left some gaps but if you have questions I’ll try to fill them in as best as possible.

References:

1. Linos E, Swetter SM, Cockburn MG, Colditz GA, Clarke CA. Increasing burden of melanoma in the United States. J Invest Dermatol. 2009;129:1666-74.

2. Bishop JN, Harland M, Randerson-Moor J, Bishop DT. Management of familial melanoma. Lancet Oncol. 2007;8:46-54.

3. Chin L, Garraway LA, Fisher DE. Malignant melanoma: genetics and therapeutics in the genomic era. Genes Dev. 2006;20:2149-82.

4. Rivers JK. Is there more than one road to melanoma? Lancet. 2004;363:728-30.

5. Friend SH. Genetic models for studying cancer susceptibility. Science. 1993;259:774-5.

6. Gordon M. The Genetics of a Viviparous Top-Minnow Platypoecilus; the Inheritance of Two Kinds of Melanophores. Genetics. 1927;12:253-83.

7. Schartl M, Peter RU. Progressive growth of fish tumors after transplantation into thymus-aplastic (nu/nu) mice. Cancer Res. 1988;48:741-4.

8. Kazianis S, Gutbrod H, Nairn RS, McEntire BB, Della Coletta L, Walter RB, et al. Localization of a CDKN2 gene in linkage group V of Xiphophorus fishes defines it as a candidate for the DIFF tumor suppressor. Genes Chromosomes Cancer. 1998;22:210-20.

9. Leroi AM, Koufopanou V, Burt A. Cancer selection. Nat Rev Cancer. 2003;3:226-31.

10. Schartl M, Hornung U, Gutbrod H, Volff JN, Wittbrodt J. Melanoma loss-of-function mutants in Xiphophorus caused by Xmrk-oncogene deletion and gene disruption by a transposable element. Genetics. 1999;153:1385-94.

11. Wittbrodt J, Adam D, Malitschek B, Maueler W, Raulf F, Telling A, et al. Novel putative receptor tyrosine kinase encoded by the melanoma-inducing Tu locus in Xiphophorus. Nature. 1989;341:415-21.

12. Gomez A, Volff JN, Hornung U, Schartl M, Wellbrock C. Identification of a second egfr gene in Xiphophorus uncovers an expansion of the epidermal growth factor receptor family in fish. Mol Biol Evol. 2004;21:266-75.

13. Schartl M, Wilde B, Laisney JA, Taniguchi Y, Takeda S, Meierjohann S. A mutated EGFR is sufficient to induce malignant melanoma with genetic background-dependent histopathologies. J Invest Dermatol. 2010;130:249-58.

The post Guest Post: Why cancer researchers think fish are cool first appeared on Deep Sea News.

Our project team has an extensive set of baseline samples representing deep-sea and shallow water habitats (see map below).  We will be merging both taxonomic expertise and metagentic data to assay the diversity of virtually all eukaryotic meiofauna in Gulf sediments, and address two key questions:

1) How unique are the meiofaunal communities in the GOM?

2) How structured are the meiofaunal communities within the GOM?

Answering these two questions will allow us to better understand the effect of anthropogenic disturbance on the meiofaunal communities. These taxa function as key primary consumers within marine ecosystems, with meiofaunal diversity and abundance exhibiting a linear correlation with primary productivity (De Troch et al. 2006). Temporal comparisons of meiofaunal communities will be invaluable for assessing spill impacts and habitat recovery.

My first mission is a sampling trip to the Gulf from September 12^th-25^th .  I’ll be going down to the University of Texas at San Antonio and Auburn University to meet with collaborators, and then heading to Dauphin Island and out on a boat to get some samples off the continental shelf.  Following that, I’ll be driving along the Gulf coast collecting some “post-spill” samples for comparison to our baseline data (The orange diamonds on the map give you a rough idea of the areas I plan on visiting).

After reading that Newsweek article, I’m interested to see if I will run into any problems in the Gulf.  Will I be kicked off any beaches?  Will my samples be confiscated?  Can I use my charm and fake English accent to get myself out of above-mentioned situations should they arise?

Even if there isn’t any drama, I will be on the lookout for tarballs, slicks, and sheens (oh my!). I’ll be sending regular updates and pictures via twitter, as well as blogging longer entries on DSN.  In the meantime, feel free to send me any questions, requests or suggestions!  The countdown begins, T-minus 6 days…

References:

De Troch, M.D., et al. (2006). Resource availability and meiofauna in sediment of tropical seagrass beds: Local versus global trends. Marine Environmental Research, 61 (1), 59-73 DOI: 10.1016/j.marenvres.2005.05.003

The post Follow Dr. Bik to the Gulf! first appeared on Deep Sea News.

For this week’s ResearchBlogCast I chose the Birky paper after reading about it on the Marmorkrebs blog by Zen Faulkes. You can listen to the ResearchBlogCast at ResearchBlogging.org, where each week Razib Khan, Dave Munger and I discuss a peer-reviewed article from the RB aggregator.

Birky, C., Adams, J., Gemmel, M., & Perry, J. (2010). Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms PLoS ONE, 5 (5) DOI: 10.1371/journal.pone.0010609

In many asexual taxa, DNA sequences alone are used to detect and assign species, but this is only meaningful in the context of a well-defined species concept that you are blatant about operating under. I say “operating under” because I personally feel that scientists need to recognize that different species concepts are useful under different scenarios or for different taxa. This is called pluralism in the species concept literature. Many biologist from the ecology and evolutionary biology are not forthcoming about what species concept(s) they are operating under when they write up their results.

The new framework being proposed draws on previous work by the authors characterizing the mode of speciation in bdelloid rotifers. They updated their model to make it more general to other asexually reproducing taxa. Birky and colleagues refer to it as the 4x rule and argue that clades are sufficiently diverged by a number of generations equal to 4 times the effective population size. At this genetic distance, speciation is deep enough to be discerned from random genetic drift and other stochastic processes. It does not have to be exactly 4 times, but is actually the ratio of the average sequence diversity between groups to the nucleotide diversity among individuals within a groups. The point being that this is when two clades are reciprocally monophyletic at a statistical probability of 95% confidence.

What these authors try to do is introduce a rigorous way to define species that is based in existing theory. They differentiate this from DNA barcoding because the barcoding approach identifies species already defined by traditional taxonomy and uses empirically determined limits, not justified by any theoretical foundations. This also differs from traditional taxonomy because the authors feel that discernible phenotypes need not be present to distinguish between species, only reciprocal monophyly.

What I don’t really understand yet is how this really differs from the phylogenetic species concepts of the 1980s and ’90s. It may be that the population genetics species concept present a more rigorous and less subjective way to define species within a phylogenetic species concept. For instance, 2 closely-related taxa that are on the verge on being an obvious phylogenetic species may be discerned by using Birky and colleagues methodology as a decision rule.

The post ResearchBlogCast #11: A Population Genetics Species Concept? first appeared on Deep Sea News.

The question I wished we asked more is: what is this species doing?  When I look at marine sediments under a microscope, my mind buzzes with the thought of millions of unknown genetic pathways all ecologically intertwined yet inherently isolated in each individual organism.  In the old days (circa 2005 and boho-chic fashions), understanding gene expression was limited to single species—common model organisms—scrutinized in highly artificial settings (hmm, which gene do I want to knock out of this mouse today?).  Oh, and you had to have previously sequenced the entire genome for said organism if you ever wanted a shot in hell at understanding your data.

Fast forward to the present, and researchers are embracing a new field: Metatrascriptomics.  Try to say that three times fast.  Transcriptomics of any variety is the study of RNA molecules (messenger RNAs, ribosomal RNAs, transcript RNAs and non-coding RNAs) present in a cell at any given time.  By sequencing RNA molecules, we can get a snapshot of the genes being expressed in a cell, tissue, organism, or even whole community of organisms at a given place and time.  These type of studies used to be carried out in a limited fashion using quantitative PCR (qPCR) or microarrays, but new sequencing technologies (454, Illumina) now allow us to sequence RNA at a much grander scale: we’re getting more sequences than ever (millions at a time) and can cover a huge taxonomic breadth (whole microbial communities).

In the past few years, Metatranscriptomics has revealed some really neat stuff about marine environments, which Mary Ann Moran has summarized in a stellar review article.  For example, Hewson et al. described the expression profile of a key cyanobacteria species (Crocosphaera watsonii) whose biology was poorly known but played a key role in nitrogen fixation in marine environments.  In another study, Poretsky et al. analysed mRNA transcripts to describe the activity Pacific bacterioplankton communities across day and night.  They found evidence that these organisms invest heavily in energy acquisition and metabolism when the sun is shining, but shift over to producing important molecular components (amino acids, vitamins, membranes) once immersed in darkness.  How cool is that?

These new approaches are once again highlighting how little we know (when isn’t that the case in science?).   It appears that any typical pelagic microbial transcriptome currently contains a huge proportion of previously unknown gene products—Gilbert et al. reported a whopping 91% of large gene families that appeared to be novel!

These studies just reinforce my (somewhat compulsive) desire to sequence everything in sight.  That, and remind me to start carrying around an emergency pipetting kit, just in case.

References:

Gilbert, J., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., & Joint, I. (2008). Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities PLoS ONE, 3 (8) DOI: 10.1371/journal.pone.0003042

Hewson, I., Poretsky, R., Beinart, R., White, A., Shi, T., Bench, S., Moisander, P., Paerl, R., Tripp, H., Montoya, J., Moran, M., & Zehr, J. (2009). In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii The ISME Journal, 3 (5), 618-631 DOI: 10.1038/ismej.2009.8

Moran, M.A. (2009). Metatranscriptomics: Eavesdropping on complex microbial communities Microbe, 4 (7), 329-335 Open-Access PDF

Poretsky, R., Hewson, I., Sun, S., Allen, A., Zehr, J., & Moran, M. (2009). Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre Environmental Microbiology, 11 (6), 1358-1375 DOI: 10.1111/j.1462-2920.2008.01863.x

The post If I had my way, we’d just sequence everything first appeared on Deep Sea News.

The western Pacific is broken land, plates are crashing every which way creating earthquakes and volcanoes from Russian Kamchatka to New Zealand. At these volcanic arcs exist a unique and abundant flatfish at hydrothermal areas. Symphurus thermophilus was described as one species along the entire western Pacific volcanic arcs, which begged the study that Tunnicliffe and colleagues did – study how divergent population of this species are! The authors used 2 genes, COI and 16S, both commonly used in population genetics studies, on Symphurus species from near Japan and near New Zealand. They found that between those individuals inhabiting the Mariana Arc and those inhabiting the Tonga-Kermedec arc, population were diverged by 9% and 14% for COI and 16S, respectively.  Previous Barcode of Life projects found 3% (butterflies) to 9-10% (fishes) divergence to be sufficient for delimiting new species. Within each arc system, populations appeared to be well-mixed, but there are indeed migrants between arcs.

Why is this study cool? Besides their barcoding of the vent flatfish from Japan and New Zealand vent, they used a real integrative approach with morphology, gut contents, ecology and behavior to conclude that this is likely to be 2 or 3 species total.

Tunnicliffe V, Koop BF, Tyler J, So S (2010) Flatfish at seamount hydrothermal vents show strong genetic divergence between volcanic arcs. Marine Ecology doi:10.1111/j.1439-0485.2010.00370.x

This paper by Milner and colleagues studied whether male fiddler crabs could sense there were receptive females around when they could no see them by observing the courtship displays of neighboring crabs (the fiddler crab claw wave). In a simple, but elegant, experiment they placed a barrier in front of the males so they could not see if receptive females were present or not. They found that the number of claw waves by males increased (see graph on left) in the presence of females with or without barriers. This means that they were eavesdropping on the courtship behavior of their neighbors in order to prepare themselves for waving their arms about madly to attract the opposite. Sound familiar?

Why is this study cool? OK, let’s be honest here, I picked this article because of the title: “Eavesdropping in crabs: an agency for lady detection”. WIN!

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Is it a coincidence that there were mass die-offs of urchins off Nova Scotia after 2 eastern US hurricane landfalls? Scheibling and colleagues find it curious at least and show interesting data correlating the timing of two hurricanes and the urchinicide, which occurred 2-3 weeks after the hurricanes made landfall. They found that disease-causing amoebas were present in dying urchins, confirmed it by taking urchins form colder waters, a more harsh environment for the Paramoeba to develop in, and exposing them to water from infected urchins. All urchins died off between 17 and 21 days from all treatments.

Why is this study cool? They show that “… hurricane-induced mixing can deliver a nonresident pathogenic agent to the Atlantic coast of Nova Scotia.” If a pteropod flaps its mantl “wings” off of Florida is there a mass urchinicide in Canada?

The post The Tide Pool: Divergent Flatfish, Eavesdropping Fiddler Crabs, Hurricanes Kill Urchins first appeared on Deep Sea News.