Papers of the Week

26 08 2012

Note: It’s come to my attention that many readers don’t have access to these papers. I have access to PDFs of most; those I don’t, I e-mail my friends who beam it by e-mail. I know we’re all strangers, but you can be my friend too, my e-mail’s here. If you get what I’m ambiguously saying (papers *are* copyrighted works, I don’t need the academic publishing moneysuckers to turn their evil mandibles on me).

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.

Some papers are tagged for easy finding using your browser’s find (Ctrl+F):

  • [OA] is for open access papers, those you can read for free.
  • [imp] is for papers that I perceive as particularly important to have.

86 papers this week, 4 special issues. Breakdown below.

Index:


Special Issues:

In Europe, the Magdalenian is the latter part of the Palaeolithic, from 17000 to 13000 BP, and was the time when humans were hunting mobile grazers (horses, reindeer). Humans formed settlements, with lots of hearths known from the time. If you’re interested in archaeology, I guess you’ll want to read these papers.


Arthropods:

Being the organs critical for insect flight performance, wings are always under very high selection pressure. This is why wing venation patterns can reliably be used for species-level identification in most flying species – they are always uniquely modified to suit the specific habitats and ecologies of their species. Given that dung beetles are some of the most ecologically diverse phylogenetic groupings, this makes them ideally-suited for studying the evolution of wings (hind wings, since the front wings of beetles are already modified to the elytra) under different selection pressures. This is what this paper is about.

The development of onychophores (and tardigrades) is important to investigate thoroughly in order to clarify the basal evolution of arthropods. This is another paper to add to this segment of the literature.

For more on development in onychophorans in this context, see Eriksson et al. (2009). For the same context but specifically in terms of the central nervous system and the head (one of the critical areas of arthropod evolution), see Eriksson & Stollewerk (2010), Mayer & Whittington (2009), and Eriksson et al. (2003).

Scopulae are pads of setae on the legs of spiders. They look like brushes and are used as adhesive pads, used to give spiders their ability to walk on smooth vertical surfaces or to grip to their prey. In some spiders, the scopulae also act as contact chemoreceptors. Anyway, this paper serves as a small atlas for scopulae from 11 families.

For more on scopulae, see Niederegger & Gorb (2006).

The title states the result of this study. This is a case of aposematism, warning colouration, although not as striking as the famous poison dart frogs. If you’re interested in the evolution of aposematism, see Lindström (1999), Speed & Ruxton (2005), Ruxton et al. (2008), and Brodie & Agrawal (2001).

I always enjoy reading genus-level and species-level morphological systematic studies, but that’s just the organismal biologist speaking. Not much to say about this paper. If you want to read more on the evolution of sexual size dimorphism in orb-weavers, see Hormiga et al. (2000).

Ever since I started working with vernal ponds, I slowly started falling in love with fairy shrimp. Their cryptic diversity, their incredibly quick life cycle, their metapopulation dynamics. All very fascinating stuff. I highly-recommend working with them, they’re awesome. Just thought I’d mention this while I had the chance, since papers on them don’t come out all that often.

Many alpheids, snapping shrimp, burrow into soft, muddy sediment to form U- or Y-shaped burrows, often co-inhabited with a mutualistic fish. This paper describes the association of Alpheus rapax with a gobiid fish, as well as a new type of behaviour, described thusly in the abstract:

The display was only performed in newly molted individuals while within their respective burrows in the presence of light. The display consisted on the following repetition: shrimp shifted its entire body forwards, with the cephalothorax angled downwards with respect to the pleon and both chelipeds extended forwards and towards each other; body jerked rapidly backwards with pleon curled and walking pereiopods extended; cephalothorax angled upwards, while the chelipeds were spread apart and moved backwards; and continuous undulations of pleopods.

If you’re interested in the Malpighian tubules, the insect equivalent to the kidney (kind of), see Pannabecker (1995).

Important only in the sense that it’s the oldest record of a lophopid, a small family (130+ species) of fulgoromorph.

The current diversity of aeshnopteran dragonflies is but a small vestige of their past diversity – many families are now extinct. This paper just puts modern biodiversity to shame some more.

I’ve written a post about fireflies here, including a section on their flashing communication with refs. This paper reports on a species where it’s the female that initiates courtship, and that it’s the duration of the flash that males take into account.

For background on how Drosophila processes odour information, necessary to understand this paper, see Masse et al. (2009).

This paper reinforces the need to study an island like Cyprus and its arthropod fauna (interested?  Contact me, I’m always looking for contacts who can help, especially if you have a source of funding!). It finds that biodiversity in European tenebrionids follows temperature gradients, with higher temperatures harboring more species. This means Mediterranean countries are those with the most species, and the large Mediterranean islands, including Cyprus, played a special role as glacial refugia and postglacial colonisation sources.

I still haven’t worked on the My Research tab, but if I did, you’d see one link to my current work on antlions. A colleague spent a painstaking three months recording the movements of antlion larvae on a park trail using a grid, resulting in an enormously detailed dataset. my job is to first of all find a way to statistically analyse this data (I’m using point pattern analysis on steroids), and then to interpret it. Substrate density is one of the factors to take into account: this paper finds that antlions much prefer less dense sand to build their pits in, probably because it makes it easier to build and because such substrates are better to catch prey with.

If we accept an ant colony as a superorganism, then the tunnels count as part of its extended phenotype. They’re very important, tailored to the specific colony, its geography, and its constituents, so there is a valid reason to investigate the effect of different-sized workers on its construction and structure. This paper finds that while fire ants do show some variety between different-sized worker tunnels, the critical features are always the same. They’re pretty good architects, these creatures.

For more ant ant tunnels and their construction, see Buhl et al. (2004, 2006), and Minter et al. (2011).

I described the special flight muscles of insects in this post.

The process of silk-making in spiders is incredibly complicated – it’s not just secreting and shooting it out of the spinnerets. The effectiveness of the silk is determined by many factors, even something as seemingly innocuous as the nutrition of the spider. For one thing, from the biochemical side, a lot of processing takes place, the effects of which are detailed in this paper.

The antennules are one of the most important chemosensory structure of decapods, being connected directly to the brain through two pathways: the aesthetac/olfactory lobe pathway, and the non-aesthetac/lateral antennular neuropil pathway. The former is of interest for this paper, with the aesthetacs being the main chemical sensors; in this species, they’re innervated by ~175 neurons each. What this paper studies is how aesthetac positioning and antennule movement allows the crayfish to sense as much of its environment as possible.

Any paper with “arthropod” and “head” in the title must be saved, because it bears important data on the arthropod head problem, and thus for the resolution of arthropod phylogeny (the only taboo topic on this blog!). Case in point, this paper is a standard paper on gene expression in a myriapod embryo’s head, yet one can still write a sentence at the end of the bastract with such wide-ranging implications as “This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.”

If you want my advice, stay away from the area of higher-level arthropod phylogenetics. I live here, and it’s a place where only madness lies. Or do I say this to reduce competition and thus give me higher chances of finding the correct answer and gaining fame and glory among the handful of people here while the rest of the world toils away with stuff that’s actually important?

The Xiphosura are the horseshoe crabs and their relative. Comically stupid animals. This paper examines their ontogeny and the bearing it has on how we consider their evolution, taxonomy, and systematics.


Ecology:

This is a comprehensive study testing the three main hypotheses for the occurrence of sexual cannibalism in spiders (extra nutrition; side-effect of aggression; mating preference for suicidal males). The results support the first two hypotheses, with more support for the first one, with more offspring hatching from better egg cases in the well-fed cannibals.

This study finds that, contrary to what might be thought, fiddler crabs that have to use a smaller and weaker regenerated claw for their mating display and fight don’t experience an increased amount of losses, meaning that they’re able to compensate by “fighting harder”. I like to picture such a crab as a protagonist in a Sylvester Stallone movie.

This looks like a great R package. I installed it and will be playing around with some sample Cyprus datasets from my research to see what its capabilities are.

This is a very interesting paper, especially considering my research in Cyprus, showing that different evolutionary processes occur on islands than on mainlands. This is just one research paper using frogs though; I have to wonder if and how the results would vary using more mobile organisms, or organisms with less strict environmental preferences. If I had the barest amount of funding, I’d do it using my Cyprus datasets.

A good paper to outline some basic errors one finds in the molecular ecology literature.


Environmental:

I always go out of my way to buy GM foods, even if it’s just to spite the fools who buy into the whole bullshitty organic movement, because there is one thing that has to bet set straight: the only future sustainable agriculture has is with GM. Organic is too wasteful and too dirty to be maintained. Fear over the safety of GM crops have until now been completely unfounded, and risks identified are promptly taken care of and involved strains discarded after the very stringent regulation by all food safety administrations. One of the main fears that anti-GMOers parrot is that the genetic material will somehow contaminate “natural” crops by lateral gene transfer. Considering just how rare HGT occurs in multicellular organisms, especially angiosperms, this is just pure silliness. However, it’s a different ballgame with unicellulars, where HGT is pretty routine. Hence this paper is a warranted call for safety with the potential of GM-cyanobacteria to contaminate their wild counterparts is actually a real possibility.

Aedes albopictus, the Asian tiger mosquito, is one of the best success stories for biological invasions. From the mosquito’s side at least. In just a few decades and spurred on by anthropogenic introductions, the species went from its original distribution in the Western Pacific and SE Asia and spread out to the Middle East, Africa, Europe, both Americas, and the Caribbean, and is now commonly viewed as the most common pest mosquito. It’s a worrisome trend, because it’s a vector many disease-causing arboviruses, including the dengue and chikungunya, although evidence for actual disease transmission isn’t so common. Anyway, this paper looks at whether the species will be able to stay in Europe as the climate changes, important to know for predicting the changes in pathogens and ifnection rates, an important sociological factor that has to be accounted for in global warming effects on humans.

For more on the spread of the species, see Benedict et al. (2007), and Medley (2010).

One of the main concerns with building any kind of factory or power plant near water isn’t only pollution, but also the release of hot water. This is particularly the case with nuclear power plants, who don’t release any sort of pollution anyway. This paper finds that brain corals aren’t really affected by this: they adapt by changing their symbionts to more heat-tolerant ones. Elegant solution.

Everything that you throw away will eventually go back into the environment. This is something that has to be taught to kids from a very young age. It should also be demonstrated, although I don’t know how that can be done (I don’t think about methods for teaching kids, I much prefer undergrads and teenagers). Even stuff that’s “biodegradable”, or made from biological materials, has the potential to be toxic. This paper brings up one class of garbage that, apparently, hasn’t been well-researched: cosmetics and drugs, and what happens when they’re disposed of in freshwater. They obviously have an effect, and it’s up to aquatic ecologists to study them. In an ideal world, they shouldn’t have to do this, because people, garbage disposal companies, and corporation in an ideal world wouldn’t be lazy and idiotic enough to dump their drugs in water.


Evolution:

The Zero Force Evolutionary Law proposed by McShea and Brandon states that the default course of evolution is to increase complexity. It’s an intriguing claim, although I don’t quite buy it. This paper can help you on your way to thinking critically about it.

If you want to know more about the ZFEL, it was first proposed in a 2010 book, Biology’s First Law. Brandon (2010) is a favourable paper on it, Bromham (2011) is a very fair critique.

Back in 1896, psychologist James Mark Baldwin wrote a book, A New Factor in Evolution, in which he proposed that individual organisms could acquire adaptive responses to the environment and pass them on; this was part of his greater view of organic selection. This has since been termed the “Baldwin effect”. He said it was at least as important as natural selection, a sentiment echoed by people such as Dan Dennett (Evolution and Learning). Renowned palaeontologist and co-crafter of the Modern Synthesis, George Gaylord Simpson, said in 1953 that it’s so rare that it shouldn’t be taken into account by evolutionary theory. Most now accept that there is merit to the Baldwin effect and organic selection, its general ignorance owing more to sociological factors (e.g. Baldwin’s arrest leading to the cessation of his academic career in 1908) than to scientific faults. In fact, just last year, a symposium was held by the Linnean Society about it. This paper reviews where it stands firm and where it doesn’t.


Geology:

The background to this paper is that there are two, not necessarily mutually exclusive, main hypotheses for the evolution of seawater and its chemical composition through the Phanerozoic (Cambrian to today). One states that tectonics controls seawater, with the chemistry affected by the recycling of seawater through hydrothermal vents. The other states that sedimentology is the controlling factor, specifically the transport and deposition of dolomites and gypsum. The way tor esolve the debate is through more data, and since calcium isotopes are readily available (through fossil shells and carbonates) and their properties as proxies are known, they can be used to pick out the causative factors. This paper examines the trend of calcium isotope excursions, and concludes that the second hypothesis is the more likely one, linking the patterns seen in the record with changes in palaeoclimate and the biosphere.

The Neogene (23 Ma to today) was a time of frequent environmental changes, with climate, fluctuating sea levels, and tectonics all creating constantly different stresses for the biosphere. In this paper, these changes are quantified and compared between North America and Eurasia, finding that North America became aridified 5 Ma earlier than Eurasia, and linking these changes to the terrestrial faunal migrations that characterise the Neogene.


History of Science:

Galen is a critical person in the history of biology, and especially of medicine. It was Galenic medicine that ruled from Antiquity until the advent of modern medicine (the “humours” and all that). Human anatomy was revolutionised by Galen. So it’s a good idea to get acquainted with the man if you didn’t know about him. Sure, his research is extremely outdated and wrong, but that’s just the flow of science; his contributions were massive.


Palaeontology:

The most well-known fossil arthropod eyes are the eyes of trilobites, which are always fossilised since they’re made of calcium carbonate (a unique construction). Otherwise, they’re known from Konservat-Lagerstätten – sites of exceptional preservation – where they can be preserved to varying levels of accuracy (my BSc. fossil, for example, was so complete that I could count the number of facets and even estimate its field of vision). This is how we know that Opabinia had 5 stalked eyes, or that Anomalocaris‘s eyes were so big. This paper provides some more exceptionally-preserved eyes, from the Chengjiang “lobopods”, Luolishania and Hallucigenia. Considering the similarities between lobopods and onychophorans (velvet worms), it was always thought that they would have a similar visual system with simple ocelli. Instead, these two lobopods have proper lateral eyes as are known from the euarthropods. It’s an interesting addition to the mosaic of early arthropod evolution.

For more on trilobite eyes, see Clarkson et al. (2006). For more on Luolishania, see Ma et al. (2009).

“Molecular fossils” are chemical compounds found in rocks that are derived from a biological origin; usually they’re specific organics compunds. Despite caveats (the risk of contamination, avoided if using proper extraction and sample storage methods), they have proven to be very useful in the search for life in the Archaean, where the line between geological feature, mineral build-up, and bacterial fossil is too thin to allow unambiguous identification of bacteria or other biological structures. This paper presents a couple of new ones that can be looked for.

This is an interesting paper showing that unlike what is traditionally thought, deep-sea vent faunas aren’t shallow marine faunas that took advantage of changes in ocean temperature to expand to the deep sea and then got trapped there. Instead, it shows that deep-sea vent faunas come from the deep sea already.

Important if you’re into dromaeosaurids, the close relatives to the birds. They were slender predators from the Lower and Upper Cretaceous, ranging in size from mockingbird-size to emu-size, and best known for the recurved claw on their second toe (think raptors).

The colour of insects can arise in two ways: pigmentation or, more commonly, structural colouring. The latter is where colour arises because of special microstructures and relief that causes light to be bent and messed around with in specific ways to produce colour. The most well-known examples are lepidopteran wing scales and metallic beetles. Because such colouring is mechanical and not dependent on biochemistry, the likelihood of it being preserved is subsequently much higher, and this paper clarifies how this happens in many different localities (one of which I’ve written about before).

For more on structural colour, see Parker (2000).

This paper reveals that non-avian dinosaurs had their peak biodiversity in the temperate areas of the globe, not the tropics or the Equator as would be expected from today’s distributions. The explanation isn’t only that climate was less significant, but also that back then, that’s where most of the land was, and given their body sizes, they probably needed more land to be able to spread out properly wihtout getting squished into extinction by competition.

I will be using this paper as part of a palaeobotany or palaeoecology required reading list and course, should I ever get the opportunity to do one. The drawings make it great to demonstrate the basics of palaeoenvironment reconstruction using plants.

Charcoal is the easily-fossilised remains of burnt plant tissue. Its fossilisation is so good that when derived from wood, cellular structures are most often preserved. The presence of charcoal in the fossil record is a tell-tale sign of wildfire; lots of charcoal means regular, probably seasonal wildfires, and can event hint at higher atmospheric oxygen levels. This paper demonstrates how finding charcoal leads us to modify our ideas about the palaeoenvironment.

For more on charcoal in palaeontology, see the thorough review in Scott (2010).

The Green River Formation is one of the most famous and celebrated fossil localities, a fossil lake system impeccably preserving fish, tetrapods (including reptiles and birds), and many insects (including ants and caddisflies). This paper explains the taphonomy in Green River. I classify it as important because Green River is quite a spectacular place yielding important fossils.


Philosophy:

I’m a bit suspicious of the claims in this paper (as I am with most of philosophy, it’s a bit of a masochistic pursuit that I keep reading this stuff), but can’T quite point my finger on where my problem is. It’s pure philosophy, so YMMV.

Species concepts are just about the only philosophy of biology debates I enjoy reading about, probably because I don’t consider it a philosophical topic. Here’s a random smattering of other papers on the subject: Ereshefky (2010); de Queiroz (2005); Wake (2002). And a good book is Richard’s 2010 book, The Species Problem: A Philosophical Analysis.


Phylogenetics:

The very first serious girlfriend I ever had was a linguist, and she introduced me to this wonderful world where words, letters, and sounds are characters used in phylogneetic analyses. Finding out that phylogenetics can be applied to something other than biological characters was something that I found really exciting, and I went on to try and apply it to such things as moral and social structures, as well as creation myths. This is just an example of how this stuff works, particularly neat because besides phylogenetics, it also incorporates biogeographic methodology. I have no idea whether the results make sense or not though, this isn’t my field. You can go to this great website for more information on the paper and its insights.

How to read a phylogenetic tree is the most basic skill in a biologist’s skillset, but it is one that has to be taught and cultivated so that it can be used in any context and with any tree, no matter how wonky its presentation may look like. It’s the same as learning how to read a graph, but much more complicated. This paper provides some more insights into where problems in tree interpretation may arise.

The excellent The Genealogical World of Phylogenetic Networks blog occasionally has posts on interpreting trees and other phylogenetic diagrams. See Baum et al. (2005) for a summary of tree-thnking.


Zoology:

I wrote about regeneration in this post, if you want some general background before reading this paper.

The evolution of the unique penguin ecology was accompanied by partly extreme modifications. They have a special integument with scale-like feathers keeping them insulated and waterproof. Their visual system is attuned to underwater vision. Their wing joints are stiffer than other birds’ to enable swimming. The loss of flight has led to a reduction in wing musculature. Contrary to other birds, they have dense bones to avoid floating. This paper provides data for how their nervous system changed along with all the other modifications happening.

For more on the investigated penguin fossil, see Bertelli et al. (2006).

I like this paper despite being about fish because it’s so complete.

Adding a keyword here in case anyone searches for this stuff: geometrical morphometrics.

Another paper to add to the “invertebrates aren’t doofus machines” pile of papers, useful for debunking the idiotic propaganda put out by Big Primate.


Actions

Information

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Connecting to %s




Follow

Get every new post delivered to your Inbox.

Join 114 other followers

%d bloggers like this: