Bad Habits (in Lab)

Ummm...I might be guilty of some of these....

They're All Alike: The Giant Squid Conundrum

I wasn’t going to post on another paper this week but then two things happened: I saw the video of the first giant squid filmed in its natural habitat (those scientists get so excited!), and I saw the study about giant squid diversity. I posted the first above and now we'll take a look at the second.

The giant squid (Architeuthis spp.) is one of the largest invertebrates and lives in the deep sea. It was first described as Architeuthis dux in 1857 by Danish naturalist Japetus Steenstrub, but since then, as many as 21 nominal species of Architeuthis have been described. The descriptions of this creature have primarily come from remains found washed up on beaches, found floating on the ocean surface, caught by deep-sea trawling activity, or in the stomachs of sperm whales (Physeter macrocephalus). It wasn’t until 2004 that a live specimen was observed in its natural habitat, and earlier this year that the first video footage was published (although not the in-the-natural-habitat version above). It is estimated that female squid reach a total length of 18m (59ft) and males reach slightly smaller sizes. The giant squid is globally distributed, with the exception of polar regions. They feed primarily on fish and smaller cephalopods. Studies of carbon and nitrogen isotope profiles of the upper beaks suggest ontogenetic diet shift earlier in life (smaller to larger prey items), and carbon isotope composition remains constant in food sources indicating that the squid inhabit relatively small, well-defined and productive areas. The predation of adult squid by sperm whales suggests that squid population size must be large enough to support such a large whale population, although this has never been proven.

There are some rather obvious difficulties in studying giant squid using conventional, observational techniques. So other techniques must be utilized. Enter, DNA. Recent advances in DNA sequencing techniques have made it easier, quicker, and more economical to sequence long stretches of DNA. The role of DNA sequencing is becoming more and more important in phylogenetic and population biology studies. It allows you to assess the number of species, examine the amount of genetic variation, and describe population structure.

In a new paper in the Proceedings of the Royal Society B: Biological Sciences, researchers collected 43 Architeuthis soft tissue samples from the carcasses of dead animals across their known range. They extracted DNA samples from the specimens to analyze the mitochondrial genomes (mitogenomes) and levels of nucleotide variation. They generated mitogeome datasets using several strategies, depending on the quality of the DNA in each sample. I’m not going to go into their sequencing methods – if you are a molecular biologist then you already know them, and if you aren’t then I’ll just bore you. To look at the population level of the genetic variance, they wanted to compare their samples with the fossil record of coleoid cephalopods. This is challenging considering the extremely limited fossil record for these organisms. So they used four different mutation rates to tentatively estimate a time of expansion and upper and lower bounds for the time of divergence of Achiteuthis from other squid families.

They were able to complete 37 complete and 6 partial mitogenome sequences. Remember up at the top of the post where I said “21 nominal species of Architeuthis have been described?” One pretty strong conclusion of this study is that there is only one species of Architeuthis that exists, namely Architeuthis dux (Steenstrub, 1857). The researchers found the haplotype diversity of these giant squid to be high at the mitogenome level, but the level of nucleotide diversity in these sequences was found to be extremely low, with only 181 segregating sites of a 20,331 base pair long sequence. Only the basking shark (Cetorhinus maximus) has a similarly low diversity, which is the result of a recent bottleneck. This diversity for giant squid is much lower than is seen in other squid, 44 times lower than Humboldt squid (Dosidicus gigas) and 7 times lower than the recently restricted population of oval squid (Sepioteuthis lessoniana). The high haplotype to low nucleotide diversity relationship is interesting because it shows that out of a very diverse phyla of animals, the giant squid is the odd one out. Looking at the species across its range, there was no evidence of any phylogeographic structure, which is odd considering the global distribution.

So how do you explain the low genetic diversity in comparison to the global distribution (and potentially large population size)? The authors hypothesize that it could be a low rate of mitochondrial DNA evolution, something that has been observed in other marine organisms. But a low mutation rate does not explain why mitogenome duplications maintain near 100 percent identity. The authors suggest that “perhaps the duplicated sequences form stable secondary structures, which are somehow selectively beneficial, thereby causing mutations to be under negative selection,” which would lead to “a decreased rate of divergence in the duplicated regions relative to the rest of the genome, which does not appear to be the case.” Alternatively, it could be a recent selective sweep such as a bottleneck. Bottlenecks are events that greatly reduce the size of a population, usually resulting in a large reduction in the genetic diversity of that group. If this bottleneck were followed by an expansion in the number of individuals in that population then you would see that low diversity spread amongst a large population. Modeling and analysis of data support the latter hypothesis over the former.

Unfortunately, genetic data alone can’t provide an answer as to why this might have happened. Whatever event it was, climatic or biological, it would have had to been wide ranging enough to affect a global population. Perhaps it was a sudden inflation of a population that was historically smaller. It is known that cephalopods tend to be subdominant predators, and as such, are affected by the changes in population of predators and competitors. If this small size was due to restraints on predators and/or competition and that restraint were released then you would expect such an inflation in squid numbers. Considering the effect of industrialized whaling in the 1700s to late 1800s, this is a likely explanation, but still too recent to explain it entirely. This change in predators and/or competitors could have been the result of climatic effects such as the last ice age changing. Such changes could have altered the abundance and distribution of competitors such as predatory fish. Or perhaps, rather than a bottleneck, A. dux existed historically as a single, small, geographically isolated population that then expanded globally. This expansion would have had to been in a non-ordered fashion with either nomadic adults or dispersing juveniles and small pelagic paralarvae capable of using currents to travel long distances. But if they can disperse really far then why would they have been restricted historically? The authors hypothesize that a global population existed for a considerable time, and that an average of just one individual exchanged between two populations per generation will be enough to prevent genetic differentiation between them. They believe that the wide ranging dispersal of paralarvae and juveniles on the currents of the upper layers of the oceans could achieve this. These young life stages float along with the currents feeding on zooplankton and such until they reach a sufficiently large size, after which they descend to the closest nutrient-rich deep habitat where they remain until maturation.

I think that’s a pretty good explanation. What about you?


Winkelmann, I., Campos, P., Strugnell, J., Cherel, Y., Smith, P., Kubodera, T., Allcock, L., Kampmann, M., Schroeder, H., Guerra, A., Norman, M., Finn, J., Ingrao, D., Clarke, M., & Gilbert, M. (2013). Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species Proceedings of the Royal Society B: Biological Sciences, 280 (1759), 20130273-20130273 DOI: 10.1098/rspb.2013.0273


ScienceNOW article: "Giant Squid Worldwide Are One Species"
ScienceDump: "The search for the giant squid"
Vido via Nature's: "Giant squid filmed in its natural environment"

The Rose Shank

(via Alex Culang and Raynato Castro's website Buttersafe)
note panels moved vertically for space requirements

Some Budding Yeast I Used to Grow

What a wonderfully yeasty parody.

The Character of Elements

Kaycie D. received her BFA from the Milwaukee Institute of Art and Design with a major in Animation and a minor in Illustration. For her senior thesis project she decided to take on a massive character design project that she called “Elements - Experiments in Character Design.” Her goal for this project was to design a character based on each of the known chemical elements in the Periodic Table. The project premiered at her school's Senior Thesis Exhibition from April 2011 - May 2011 for 72 of the elements, and she completed the remaining 40 elements in November of 2011.

I'll whet your appetite with a few of my favorite of Kaycie's Elements. You can see the rest over at her KCD blog and her tumblr page.

 

(via io9 and The Mary Sue)

Biological Beta Testing: Altitudinal Edition

Spatial patterns in biodiversity have always been a popular topic in ecology, and understanding these patterns helps us to address the looming threats to biodiversity.

Did you notice how I made the word ‘patterns’ plural? There isn’t a whole separate field of biogeography for nothin’. Biological diversity is difficult (some say impossible) to measure using a single metric. How do you count things? Simply by the number of species? How about rare versus common species? What about species turnover? What geographic scale are you using? How and/or do you define boundaries? Would you like me to keep going or do you get the point?

Lately I’ve noticed a surge in the number of studies that look at diversity gradients that occur along latitude and altitude. We visited the topic of latitude and diversity back in October of last year with the “Dinosaurs, Diversity, Distribution, and the LBG” post. Essentially, latitudinal gradients (LBG or LDG) occur when species richness (a simple count of species) is highest in the tropics and declines polewards (warm areas are more hospitable and produce more food). Altitudinal, or elevational, gradients are nearly as ubiquitous as latitudinal gradients, and they have many of the same characteristics. As you go up in elevation (as on a mountain) the temperature gets colder and habitat areas and the communities they support become smaller and more fragmented. Gradients such as these are overall patterns. Now mix them with diversity indices. In 1960, R.H. Whittaker described the terms alpha diversity (α-diversity), beta diversity (β-diversity), and gamma diversity (γ-diversity). Basically, the total species diversity of a geographic area (γ-diversity) is determined by the mean species diversity at the local, within-site or within-habitat scale (α-diversity) and extent of change in community composition between sites (β-diversity). These definitions have been much argued over (see Tuomisto 2010), and we won’t get in to that. We are going to focus on beta diversity (β-diversity), also called species turnover or differentiation diversity. It is a measure of how different sites are from each other and/or how far apart they are on a gradient of species composition. Factors that drive β-diversity are very important, very poorly understood, and very much argued over. Is it dispersal limitation? Habitat specialization? Environmental heterogeneity? The studies published so far seem to lean toward multiple processes operating at various scales. *sigh* Isn’t that always the way? Observational and experimental studies have shown that impacts on β-diversity vary with productivity. So it would make sense to test this in relation to altitudinal and elevational gradients.

A new study to be published in Global Ecology and Biogeography looks at how local community processes may create an altitudinal pattern of β-diversity. Their study site was the Shiretoko National Park in north-eastern Hokkaido, the northernmost island of Japan. In addition to being one of the richest temperate ecosystems in the world, the area is characterized by sharp altitudinal changes in forest structure and productivity as a result of strong winds on the western side of the mountains. The researchers chose this western side to measure the diversity of woody plants and mites (Oribatida) in mature stands where they set up seven plots (each containing 10 subplots) at different altitudes. For the woody plants they recorded the number of individuals taller than 0.5 m, measured the girth at breast height (GBH), estimated the total basal area (BA), recorded canopy height (CH) of the stand, measured the diameter and length of all coarse woody debris (CWD), measured understory light, took soil cores to extract the mites, removed roots from the soil samples, measured the thickness and dry mass of the soil surface litter (A0 layer), collected leaf litter, measured water content and pH of the litter, and the carbon-to-nitrogen (CN) ratios of the litter and soil. They then calculated the β-diversity of the two organism groups for each altitude. So as to take into account the dependence of β-diversity on gamma diversity (γ-diversity), they used null modeling. This type of modeling “randomly shuffles individuals among subplots while preserving γ-diversity, the relative abundance of each species per plot and the number of individuals per subplot” which enabled them to estimate how much observed β-diversity differed from expected β-diversity. They also calculated a β-deviation value for each altitude. This is equivalent to a standardized effect size, indicating the magnitude of the deviation from what you would expect of a random (stochastic or by chance) assembly process.

First we’ll hit the results for the oribatid mites. These results showed the altitudinal gradient of β-diversity to be less evident than it was for the plants, and β-deviation showed no altitudinal gradient. That said, they found β-deviation to always be greater than expected in all locations for both woody plants and oribatid mites. In woody plants, the magnitude of β-deviation increased with altitude, suggesting that deterministic processes dominate in low-productivity, high-altitude stands, the role of these processes increasing with decreasing productivity in plant communities. The authors conclude that their results support the hypothesis that “the mechanisms underlying community assembly (e.g. niche versus neutral) play an essential role in creating biogeographic patterns of β-diversity.” They found that niche-based processes (species correlate with environmental variables, the conditions in which the species can persist) govern high-altitude stands, particularly when they included the plants growing in lower layers in the analysis. They found similar results when they calculated β-deviation along a stand-structure gradient with basal area, not altitude, particularly when small understory plants were included. This suggests that “given the altitudinal changes in stand structure, the role of understory plants in deterministic assembly becomes more dominant with altitude.” So those little guys really make a difference! Why? Well, considering that light is a precious commodity, low-elevation, structurally well-developed stands have higher competition for available light, especially for those little understory guys. This fierce competition isn’t so fierce in the higher altitude sites where the upper canopy isn't there to usurp all of the light for itself. This favors a greater, more diverse understory in higher elevations. Again, the authors speculate that this greater high altitude diversity is due to fine-scale niche partitioning, which allows more individuals to exist together.

Okay, so that is a pretty good explanation for the high altitude communities. Now what is going on at low altitudes? Well, there you have to take the site’s history a little more into account. What made these stands so “structurally developed” and generated this stochasticity? Consider this: The canopy trees of these forests colonized before the understory individuals, negatively affecting understory species by reducing the availability of space and resources. You then see a relative dominance of these big-ole-bully trees (that’s a technical term, you know) and a one-sided competition scenario.

Did I scramble your brain and make you hate biogeography yet? Can you see any sort of overall conclusion here? Lemme help you out…

β-diversity is dependent on community processes and shaped by local factors within the landscape. The species in a place use what is in a place.

Do you agree?

Mori, A., Shiono, T., Koide, D., Kitagawa, R., Ota, A., & Mizumachi, E. (2013). Community assembly processes shape an altitudinal gradient of forest biodiversity Global Ecology and Biogeography DOI: 10.1111/geb.12058


(image via Japan-Guide.com)

How to Win a Climate Change Arguement

An interesting infographic. What do you think?

via Slate.com via Climate Desk