Papers of the Past Two Weeks

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Sorry for missing last week, my brother was getting married during the weekend, no time for such frivolities. I’ve added a new section, the Must Read section, to compensate for the mammoth size of this week’s post. It contains what I would usually tag as [imp], and any particularly cool papers that would be of interest to the layman as well. I’ll probably be keeping it permanently though.

This is just a listing of papers published this week that piqued my interest (taxonomy excluded), with personal comments and further reading recommendations whenever appropriate. Interdisciplinary papers sorted according to personal opinion. Papers ordered only by their appearance in my inbox. For PDFs, e-mail me, I get most of them. You can request an in-depth analysis of any paper and I’ll do it as I get the time.

Open-access papers, those that are free to read/download even without an academic connection, are tagged with [OA] for easy finding with your browser’s text search (Ctrl+F).

135 papers, 5 special issues. Breakdown below.

Index:


Must Read:

So, in my post/lecture on the origin of life, I came out pretty harshly against the Schopf camp, saying that the Apex Chert “microfossils” are pseudofossils, armed with evidence from a paper that was new at the time. This debate, as hinted at in the post (and more clearly explained in the actual talk), has been going on for years now, and this is the latest counterstrike by Schopf. And… it’s a good one, actually, once again bringing in new technology to give us even more detail. Skeptics will be skeptical, and the title isn’t definitive. But this is still a very good comeback, and I admit I’m less skeptical.

Regardless of whether they’re pseudo or real, the assertion in the last line of the abstract, that ” it seems clear that microbial life was present and flourishing on the early Earth ~ 3500 Ma ago” is very likely to be true, whether the fossil data is there to back it up or not (we have other, geochemical, lines of evidence).

A critical review on the science of experimental evolution, including its limitations. Very useful. Refer to Garland & Rose’s 2009 book, Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments, for more on experimental evolution and how to do it.

Of the non-arthropodan fossils of the Burgess Shale, among the most important are these two: Odontogriphus and Wiwaxia. The latter is a weird animal covered in large spines, the former a soft-bodied flattened creature. Most authors have placed them somehwere in the stem of the Mollusca, although there has always been a possibility that they were more close to annelids. This paper puts those doubts to rest, confirming that they were stem-group molluscs on the basis of the detailed study of the mouthparts presented. They bear the most resemblance to a radula, fit for grazing.

This is a review of the immune system of corals, so I place it here because of its timeliness. While corals don’t have cells that act only as immune cells, they have some that are incredibly specialised, with allo- and xenorecognition, and killing mechanisms, so the animals are by no means defenceless. This review is important at this point because it’s the first one that brigns a lot of disparate information in one place, so it’s a good thing to have.

This is very cool. Pupae of the rhinoceros beetle Trypoxylus dichotoma live in the soil where they are vulnerable to any predators, such as predatory larvae of other insects. So they’ve evolved a defensive mechanism whereby they produce vibrations mimicking vibrations produced by predators of the larvae, causing the larvae to stay put for ~10 minutes. A very good use of deception.

Amazing stuff – the spectacular amber arthropod fossil record has just been extended by 100 million years, with the finding of a couple of flies and mites in 230 Ma Italian amber.

It’s a bit on the technical side, but this paper is important because it emphasises the importance of thinking about your methods when doing molecular phylogenetics, rather than just copying from another paper, doing a gene-tree and treating that tree as a species tree (these may seem like obvious msitakes, but they are all too common).

Crematogaster is a pretty species-rich genus, containing over 450 species distributed in the Neotropics, Hoalrctic, and Palaeotropics, living in dead tree bark, or on dead branches and twigs, or in/under moss, modifying woody material to make nests (although temperate species tend to be standard ground- or leaf-nesters). This paper’s a comprehensive review of their evolution.

A challenging paper, but I put it here because it’s potentially groundbreaking. I’m not convinced that multicellularity is shared that far back and still hold on to the traditional view that animal multicellularity is a unique condition possibly derived from the choanoflagellate condition. But it is a solid paper with good further research suggestions, so I willconsider myself intrigues by the other possibility.

Must read for the working scientist, since we’re judged by a variety of nebulous and unreliable metrics, such as this h-index. On the one hand, I understand the need to have a quick number to judge a scientist’s contribution. On the other hand, it doesn’t take much experience in academia to realsie that getting such a number and having it be meaningful is simply not possible, at least not for all scientific disciplines. Some papers are citation classics because they’re general reviews. Some papers are cited all the time because they’re a widely-used statistic or bioinformatics program. Some papers aren’t cited at all because they’re a taxonomic revision not useful to anyone outside of taxonomy and systematics. Yet the value of each of these papers is equal at face value, and the importance is relative to the individual researcher, but no conceivable and existing citation metric can judge these nuances. And let’s not begin with things like impact factors that encourage publishing ultra-short papers with a tiny methods section in tabloids like Science and Nature, while discouraging in-depth monographs in lower-ranked journals, even if the quality of the paper is much higher. My suggestion is to do away with all these silly metrics and judge everyone on a reading of their publication list and the projects listed on their CV (I add that second part not only because my pub. list is tiny). A bit of a tangential and generalised rant, but it’s relevant. Read this paper.

It’S rare for papers to be encyclopedic, but this is the only adjective I could think of to describe this one. A must have.

A historical look at how we came to our current ideas of treating cancer in an evolutionary framework.

Only putting it here for the coolness/weirdness factor.

If not misinterpreted, this is pretty awesome and spectacular, seeing in just how abysmal conditions in which life can nevertheless thrive.

Statistics and correlation of factors with the fossil record is always something to be treated with caution, with the myriad biases present in the fossil record and their confounding effects. Just a warning that even though the statistics here are solid, as is the interpretation, there is always the worry that perhaps this only applies to those organisms that are preserved and analysable, as well as their palaeogeographical areas.

A must-have for those interested in Ediacaran weirdos, since it provides a new framework for their morphology and how to describe and study it.

The state of the art.

Of interest only for those who like Archaea, which for some reason includes me.

I put it here because this will probably interest the general public as well. Hard evidence that cultural evolution is indeed faster than plain old biological evolution, even if I am hesitant about such a direct comparison given that the processes are different.


Special Issues:

REDD+ stands for “Reducing Emissions from Deforestation and forest Degradation”, a PES scheme (Payment for Ecosystem Services) in which forest land owners get paid (or otherwise rewarded) for conserving their forested land. This special issue has a bunch of case studies and reviews about its utility and success in terms of biological conservation.

For a review of REDD+, see Venter & Koh (2012).

Several cool papers in here, including some [OA] ones. Roche et al., Lafferty [OA], and McCallum are my recommendations.

Scroll down a bit to get to these papers. I was most interested in Spouffske et al..

See my post on this topic for background basics.

Winston, Schulze et al., and Sotka were the papers that got me interested.


Arthropods:

I wonder whether this is an adaptation or a spandrel. Could make for a good essay question in an evolutionary biology exam.

When your food source comprises of organisms whose relatives can commonly be pathogenic, like with leaf-cutting ants and their fungal gardens, developing a strong immune system is important. In this role, the metapleural gland, an organ unique to ants, has been considered to be of importance (in both leaf-cutters and other ants) based on several studies, for example showing that the gland’s secretions inhibit fungal growth. This paper does a standard toxicity study, seeing how the gland secretions affect various fungi, including pathogenic ones, and finding that the more virulent the fungus, the more potent the secretion, meaning that the metapleural glands are definitely useful for the healthcare of the ants.

I profiled cixiids in this post.

Interesting because it gives me something to consider for my own methodology of investigating heavy metal concentrations in my endemic insects. I will have to consider whether to dissect the guts out because metals seem to be concentrated there, or whether the gut is exactzly what needs to be looked at. (This study is only on termites, but the same generality applies in other insects.)

I discussed how some insects navigate here. This study is about how bees find their way around the hive. It’s fascinating how many mechanisms they have to orient themselves, especially when you consider how many sources of information they have to integrate and synthesise in their brains.

Onychophores have modified a pair of legs on either side of their heads into slime glands. The slime secreted is a liquid shot onto prey (small invertebrates). It then solidifies to immobilise the prey, and the onychophore eats everything (prey and slime together). The properties of the slime itself are of interest to biomaterials researchers (how it changes from liquid to solid, easy to think of practical applications of such a material), and the mechanisms of its formation is of interest to biologists, so this paper is timely because it examines what the slime glands look like.

Juvenile hormone must be the most versatile chemical in animals, followed closely by water.

This research program has produced several very interesting papers already, this one being the “culmination” of sorts. See Chapman et al. (2006) for another one.

Male nephilid spiders have quite a unique way of making sure the females don’t mate with any other male: they cut their palps off inside the female’s reproductive tract, forming a mating plug. The human equivalent is chopping your penis off inside the woman’s vagina, blocking off its entrance (the spider doesn’t bleed out though). This is an entirely voluntary move by the male (most of the time), who then goes on to also guard her physically; this paper provides evidence for the evolution of all of this, by finding that palp-less males are better fighters since they’re lighter and have more endurance. So they may be emasculated, but they make up for it with fighting ability.

I like all papers that show that, contrary to the popular trope, ants and other eusocial insects are flexible, not hardwired automatons.

Just like how I can’t have sex unless some smooth jazz is playing, insects will also go to great lengths to get to optimal breeding grounds. For great lengths, read Mediterranean to northern Europe, quite a long way for a moth.

Yes, there are moths that feed on blood, some calpine moths of the genus Calyptra. Their proboscis morphology is pretty interesting, since they need to pierce through skin; their relatives pierce through fruit, even tougher. Unfortunately, no B-grade horror movies have been inspired by these factoids.

Only for two pelagic copepod families, not all of them.

Oribatid mites are mobile fortresses, only capable of being preyed upon by much larger vertebrates (frogs and toads); beetles and ants can’t touch them, unless specialised. Their major defences are a very tough cuticle, weird body shapes, and noxious oil secretions from their opisthonotal gland. The most parsimonious explanation for all this defence is that it’s a response to predation pressure, as part of an “arms race” whicht hey’ve comprehensively won. This interpretation is supported by this paper, which uses ancestral state reconstruction to find that these defensive mechanisms have evolved convergently in oribatids.

The primary function of curicular hydrocarbons is to prevent dessication, but in many insect groups including crickets, they’ve been coopted for kin and mate recognition. This paper shows that the composition of the hydrocarbons is sensitive to diet, but the sensitivity is much higher in males. Therefore, it’s reasonable to say that they act as signals for the quality of the male and play into sexual selection.

Syntermitinae is a small group of Neotropical termites, known for having mandibulate nasute soldiers. This paper’s got a phylogeny of them.

The Randeck Maar fossil locality is a Miocene volcanic lake with a rich plant and insect fossil record, especially when it comes to bees. Because the usual characters used to distinguish species aren’t preserved though, morphometrics is the most reliable way to get species identifications comparable to extant bees.

Of interest for both phylogenetic methodology and the actual phylogeny. Gyrinids are predatory beetles recognisable in the field by their habit of congregating and swimming fast in circles, and by their eyes that are split horizontally so that the upper side can see above the water and the lower side below the surface.

The title isn’t some exaggeration. The ants referred to are Camponotus cylindricus. When confronted by an enemy, individual workers will go up to the invader and bite it to hold on. At the slightest touch, they will explode and spill a noxious yellow chemical cocktail. This paper examines the origin of this cocktail and finds some remarkable modifications of the internal anatomy of the ants: the mandibular gland, usually present only in the head, is grossly enlarged and spread all through the body.

Bergmann’s Rule is very simple: organisms at higher latitudes are larger than those at lower latitudes. There is strong evidence for its validity in many vertebrates, but as this paper shows, there is very little solid evidence for any generalities for insects. This is what I would have expected, given that the rule was first proposed for homeothermic vertebrates with their thermoregulation in mind.

See Meiri & Dayan (2003) for a review of Bergmann’s Rule studies.

There are only just over 20 species of social spiders known (not even 1% of spiders), so studying its varied origins there is an interesting exercise to see if the same things we say for social insects and vertebrates apply generally.

It’s online here.

I’ve never seen one of these guys. All I know is they’re deposit feeders.

Data from Cyprus, what a rarity.

Decapods have a very, very good antibacterial immune system. Among the present antimicrobial peptides are crustins, cysteine-rich petides that are 7-14 kDa large and unique to crustaceans, found running through the haemolymph. Smith et al. (2008) provide a review of them.

Bees are capable of learning and memorising. They have short-term memory that gets replaced by medium-term memory, and with more learning and repetition, they gain long-term memory of an activity. This paper studies differences between these two species to see how flexible their mental abilities are.


Botany:

Of relevance to my work on Cypriot endemism, since I need to know how plants bioaccumulate heavy metals before I can study them in the herbivores.


Developmental:

I like this paper because it demonstrates the dangers of relying too much on model organisms, especially highly-derived ones like C. elegans or Drosophila. Sure, you get tons of detail about the individual animal, but at the expense of reliable generability.

I gave a very rough introduction to spiralian development here.


Ecology:

See this post for basic background info.

Another study that’s nice to do with schoolkids.


Environmental:

I always try to emphasise positive aspects of environmental changes, because there always are some. For example, beach pollution is generally bad, but the extra bits and pieces do serve as habitats for hermit crabs. Similarly, the plastic we pour into the ocean does wreak havoc on marine life, but it is a good thing for one of the very few marine insects, Halobates sericeus, and any animals that depend on it.

Artificial lighting in cities not only destroys any chance of proper stargazing, it also confuses the navigation systems of insects, and according to this study, also changes the ecological communities of cities. This adds more evidence for the phenomenon now referred to as light pollution that must be taken into account properly (I notice many of those futurists who dream up of utopian green cities don’t care about this at all, for example). See Hölker et al. (2010) and Horváth et al. (2009) for more.

Also, this is a neat study type to do with schools in the city as part of an exploration of urban ecology (something I am doing with my own projects with schools this year).

I’m not a big fan of convincing climate change deniers with examples of extreme weather events or heatwaves or droughts, because it takes long enough to convince these idiots that climate and weather are two different things, and explaining the intricacies of how global warming leads to more extreme weather, including more snowfall in winter (oh my, how counter-intuitive!), would take more patience than I can spare for such paragons of human stupidity. The relevance to this paper is that it brings solid evidence for a link between extreme summer heatwaves in Moscow 2010 and USA 2011 and climate change, so I might change my tact a bit when discussing with climate change denialists.

For a blog post which reflects my hesitance to using extreme weather as a frame for climate change discussions, see this post in the excellent Collide-a-Scape blog, which also tangentially brings up this paper and its primary author.

I don’t know how trawling is still legal in any part of the world. It’s one of the most ecologically destructive practices we do, basically nothing more than bulldozing the ocean floor. Even with the promise of new species discoveries, marine biologists stopped doing this shit decades ago because the damage caused is so obvious – trenches in the ocean floor that take years to get recolonised. This paper explains the sedimentological aspects of the damage caused (no, it’s not pretty). I don’t understand how people can be so vehemently against whaling but still be apathetic towards trawling. The mind boggles.


Evolution:

One of the main hypotheses explaining the existence of ageing is that it’s the effect of damage done by free oxygen radicals produced during metabolism, damage referred to as oxidative damage. Assuming this is true, then oxidative damage should be an important factor in the evolution of life histories, and it’s this claim that’s tested in this review.

For more, see Nussey et al. (2009) and Monaghan et al. (2009).

I’m not a huge fan of the whole extended phenotype concept, but this paper I could get behind.

I’m not quite convinced of the thesis that metamorphosis can help in the study of personality… but the paper did get me intrigued. Still on the fence, I guess, but the more I think about it, the more sense it makes.

Finding examples of selfish genes or selfish genetic elements is pretty hard. I put the example of the t haplotype in mice in my natural selection post; another one is psr in Nasonia wasps, which exploits haplodiploidy to bias the sex ratios of wasp populations to promote their own reproduction. Wolbachia is another example. This paper presents another one for most insects.

This paper stresses the need for proper management in domestication – it’s intuitive that perfection of traits will involve reducing genetic diversity, but that’s also a pretty dangerous road to go down, sicne it renders a population much more vulnerable to disease. This is why at least in some cultures (e.g. in East Asia), it’s traditional to allow domesticated animals to breed with their wild counterparts.

See this post for basic background info.


Geology:

Kazakhstan’s got fossils from all the interesting (to me) times, from Neoptroterozoic and Cambrian, to Jurassic insects. So it’s useful to keep up with what even the Dark Arts of palaeomagnetism have to say about its palaeogeography.

I work on the palaeontological biodiversity of the Eastern Mediterranean, so the relevance of this paper is obvious. Spoiler alert: the answer to the titular question turns out to be yes.


History:

If, like me, you enjoy personal recollections by scientists about their work, then you’ll like this paper.


Palaeontology:

Back when I was in Germany doing my BSc. thesis, one of my lab colleagues was writing a thesis about these weirdo animals: tentaculitoids, animals living in conical, calcitic shells, well known for stratigraphical uses but otherwise mysterious. Being the resident native English speaker, I offered (was asked nicely? Who remembers anymore…) to help with proofreading, an affair that turned into a daily reading and copious correcting of large chunks of text. It was fun (it turns out I love proofreading, why I don’t do it to my own writing is a mystery to me), and it also meant I learned quite a lot on these monsters, which turn out to be quite resourceful little critters, although what they are and their way of life are still up in the air. This paper traces their evolution in the times when they were most diverse, the Silurian and Devonian..

I summarised this paper in my scientific method post.

You know the beginning of Jurassic Park, where they’re using some radar thingie to visualise the bones without digging? I’ve never seen that in practice (admittedly, I haven’t been on so many vertebrate digs either). This paper’s the first time I hear of such a method being used. Cool stuff, and another thing to gloat about for those idiots who think that palaeontology is nothing more than stamp collecting. (Yes, some people in science view disciplines as competing for who has the largest machinery.)

Two single finds of belemnites force us to review basic knowledge of such a well-known group as belemnites. This is why I love palaeontology.

See Baumiller (2008) for background information on crinoid morphology and its relation to ecology.

Very interesting. I’ll be trying this method out with my reams of unanalysed and unpublished stratigraphical data from Cyprus.

One of the famous Burgess Shale fossils, Leanchoilia was one of the “great appendage arthropods”, its great appendages characterised by having three “whips” on them. Besides its phylogenetic position, the other great debate concerning it has been about its eyes or lack thereof, with some authors saying it had no eyes and others cautiously saying it did. This paper more or less settles the issue (imo!) with by interpreting a pair of delicate stalked eyes capable of detecting movement, and putatively a pair of ocelli, a set-up very much resembling the arthropod crown group.

Pretty cool. Microconchids are tubeworms, and this association is one that’s known only from the early fossil record of aquatic plants.

It’s important not to confuse Multiplacophora and Polyplacophora, the latter being the chitons, even if they are so closely related – multiplacophorans are on the stem-group of the Polyplacophora.

General info on barnacles here.

Even if you’re not interested in the fossil record of pylochelids (symmetrical hermit crabs), this paper has the description of a new morphological feature that the authors describe, that applies to all hermits.

As above.

I currently have a project where I’m investigating exactly these kinds of interactions using a large collection of intact fossil shells collected from here.


Phylogenetics:

Adding some keywords: DNA barcode, DNA barcoding.

For the uninitiated, the Wagner method is a parsimony algorithm for building an initial tree to which more heuristics can be applied to find different trees. The way it works is simple: sequentially add the leaves on the tree, calculate the cost of the tree at every addition, keeping the ones that cost the least. As such, it’ssensitive to the order in which the taxa are added, but this can be corrected with randomisation.


Zoology:

The consequence of this research is this awesome video, Insane in the Chromatophores. Basically, squid have special cells called iridophores all over their body. Each iridophore has several plates inside, each plate oriented at a different direction, and this makes them reflect light in a special way (depending on the angle of the light hitting the angle of the iridophore plates, it can basically produce any colour it wants). By controlling where each cell goes, the squid can form any pattern it wants and this gives the squid perfect camouflage abilities. We know that the cells respond to the nervous system, since they’re controlled by acetylcholine, a neurotransmitter. But how exactly they’re moved about in precise manners isn’t know at all, since no previous experiment has managed to stimulate them manually (with electroshock or with chemicals). This is apparently the first time they manage to stimulate them by sending a specific strength/wavelength of electroshock; it turns out that the control is done by the nervous system electrically, and the acetylcholine is released as a result of the electric impulse. The video’s just a side-show from all that, they got their electric signals by taking the song and converting the audio to electricity and modulating it so that it can affect the iridophores. [Audiophiles, feel free to correct any mistakes I made with terminology.]

It seems cephalopods are pretty similar to humans when it comes to mating. 3 hours long and 30 minutes to recover.

Or at least it is so with my mating. Ladies.

I now look at cuttlefish as Two Face-like creatures.

My interest in this paper is for phylogenetic methodology, but I put it here because it may be of interest to the larger number of people who like mammals, specifically placental mammals (placentals is the crown group containing only extant placental mammals, Eutheria is the total group, including the stem-group species from the fossil record).

Aphroditiforms are worms with scales, called elytra (no relation to beetles), that live on the ocean floor at all depths and all substrates, often commensally with sponges, bivalves, decapods, or corals and anemones. Their chetae are also interesting because they sometimes act like photonic crystals, granting iridescence to the worms. Over 1200 species are found in the taxon. This paper’s got a phylogeny.

I mentioned sabellarids and their crown over here.

Putting this in the zoology section instead of the palaeontology section because as far as I’m concerned, the implications of this are for sponge phylogenetics, namely support for the traditional view for the monophyly of sponges, a view that’s been challenged recently by claims that they are paraphyletic, with the Calcarea forming a taxon on their own. By identifying more homologies in the spicules between the Silicea and Calcarea, a monophyletic Porifera gains more support (and I gain happiness, because the idea of paraphyletic sponges is hard to swallow).

Interesting. That’s all I can say – I’m not really fit to judge the strength of this paper, I’ll leave that to the coral freaks.

The mastax is one of the unique characters of rotifers. It’s their pharyngeal apparatus used to feed, and consists of trophi (hard parts) controlled by ligaments and connective muscles. The trophi are of importance for taxonomy too.

Technically, this counts as taxonomy, but since it’s a new family, I thought I’d include it too. It’s not very often that new families are discovered, after all.