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. Titles in bold are open access; abstracts are always free. Papers ordered only by their appearance in my inbox.
77 papers this week.
Index:
- Special Issues
- Arthropods
- Biotechnology
- Botany
- Developmental Biology
- Ecology
- Environmental
- Evolution
- Geology (incl. Historical Geology)
- History of Science
- Palaeontology
- Phylogenetics
- Zoology
A series of review papers on geoengineering, highly-recommended for anyone interested on the subject. I especially recommend the following papers: Geoengineering the climate; The runaway greenhouse; Marine cloud brightening; Ocean acidification in a geoengineering context.
A bunch of case studies on using algae to monitor rivers.
For the bioinformaticians.
I’ve written about photoreception in animals already. I’ll let the abstract do the commenting:
In fly photoreceptors, light is focused onto a photosensitive waveguide, the rhabdomere, consisting of tens of thousands of microvilli. Each microvillus is capable of generating elementary responses, quantum bumps, in response to single photons using a stochastically operating phototransduction cascade. Whereas much is known about the cascade reactions, less is known about how the concerted action of the microvilli population encodes light changes into neural information and how the ultrastructure and biochemical machinery of photoreceptors of flies and other insects evolved in relation to the information sampling and processing they perform.
The paper clarifies those unknown bits with the help of a model.
This is a pretty cool paper. The organisms studied are two ladybirds, Harmonia yedoensis and H. axyridis. The former is a specialist on pine aphids, the latter is a generalist that feeds on anything, anywhere. The study finds that when there are large numbers of the generalist, the specialists reproduce much less. The opposite doesn’t apply: the generalists reproduce just as much, regardlerss of how many specialists there are. What the generalists do is called reproductive intereference, and it’s hypothesised by the authors of the paper that this is what leads to the maintenance of the specialised diet of the specialist ladybird.
Hochkirch et al. (2007) show the next step in reproductive interference: the driving out of the interfered species. This then ties up with the whole issue of specialist species being more volatile (go extinct faster) than generalists.
- Behaviour and physiology shape the growth accelerations associated with predation risk, high temperatures and southern latitudes in Ischnura damselfly larvae.
Organisms from warmer, southern climates grow faster. It’s known both intuitively, and from data. But is it really the warmth that mediates this accelerated growth, or is it other factors with warmth being just a proxy? This is what this study is about, using Ischnura damselfly larvae. The results are clear from the abstract:
While the higher growth rates in the southern populations and the high rearing temperature were driven by both an increased food intake and a higher growth efficiency, the higher growth rates under predation risk were completely driven by a higher growth efficiency, despite a lowered food intake.
If you’re interested in doing similar experiments by yourself or as part of a classroom project, check out Locklin et al. (2012) for a guide on how to raise Ischnura larvae. For more ideas on how odonates can be used for studying evolution and ecology, check out the excellent 2008 book by Córdoba-Aguilar, Dragonflies and Damselflies: Model Organisms for Ecological and Evolutionary Research.
This paper describes how Böhm’s bristles, a set of sensory hairs on the antenna of hawkmoths, are integral to positioning the antenna before flight: when they’re removed, the wings hit the antenna when the flap. It also goes into the neurological details of how they work. If you’re interested in insect flight and coordination, check it out.
Humans aren’t the only social animals that get hormone-mediated mood swings. Cockroaches are similar, and their changing hormone levels are associated with the ovarian cycle (if anyone of you even thinks of drawing a contrast with women, stop now. Totally different mechanisms, physiologies, and reactions). This study shows that it’s actually sociality that can drive the changing hormone levels, not the other way around.
For more on cockroach sociality (not including termites), see Lihoreau et al. (2012).
It may be surprising to learn that something as seemingly simple as a leech has multiple ways to move about. Combined with our deep knowledge of their nervous system, this makes them an ideal choice for neurological studies, as demonstrated by this research on the neurological mechanisms underlying their crawling.
For more on how leeches move, see Friesen & Kristan (2007). For the neurology behind their movement, see Mullins et al. (2011).
I’ve written before about insect flight here, here, and here. The latter is of most interest with this paper, which deals with the aerodynamics of a dragonfly wing in flight. Insect wings are marvels of engineering – they’re tough but flexible, and this is demonstrated in flight, when the wings deform in 3D to keep the very intricate aerodynamics of insect flight possible.
See Wang & Russel (2007) for more on how the wings act during flight.
This paper is all about things I had no idea about. Interesting stuff.
- Challenging limits: Ultrastructure and size-related functional constraints of the compound eye of Stigmella microtheriella (Lepidoptera: Nepticulidae).
As I wrote in this post, the biological marvel of modern insects is their miniaturisation that tests the limits of compactness while retaining complete functionality. This paper looks at the eye of a tiny, 2mm large nepticulid, and how it works.
For more examples of tiny eyes and their functioning, see Gonzalez-Bellido et al. (2011).
The midgut is the second largest organ of any insect, where food and water (and bacteria and toxins!) come in, so obviously a very important part of insect anatomy. This paper describes how it’s built in beetles.
- First μ-CT-based 3D reconstruction of a dipteran larva—the head morphology of Protanyderus (Tanyderidae) and its phylogenetic implications.
I once saw a lecture given by Rolf Beutel (senior author of this paper) about his work using µ-CTs on insects to investigate their morphology in unparalleled detail (I was interested because at the time, I was working with µCTs with my BSc. fossils). It’s absolutely amazing, and I will always recommend every single paper that comes out from his group. Check out this one for the detailed internal anatomy of the larval head of a tanyderid fly.
- Geographical variation in adult life-history traits of the European cherry fruit fly, Rhagoletis cerasi (Diptera: Tephritidae).
- Biology of a new species of socially parasitic thrips (Thysanoptera: Phlaeothripidae) inside Dunatothrips nests, with evolutionary implications for inquilinism in thrips.
Besides the new species, this paper also hypothesises that Australian Phlaeothripinae got their inquiline lifestyle from a single common ancestor.
- From forest to plantation? Obscure articles reveal alternative host plants for the coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae).
I like this paper mainly for highlighting the importance of going back to old primary literature, most of which can’t be found online. As someone who has a knack for doing literature searches and sitting in old, dusty journal archives, it always saddens me when I see university students not bothering taking a trip to the library to get a hard copy of an article they can’t find on Google Scholar.
This makes a nice change from the usual stories of animal parasites. The museum at my old institute had two horseshoe crabs in an aquarium. They’re very stupid animals, swimming clunkily and headbumping into each other 24/7, because they don’t realise they can also swim up. It wouldn’t surprise me if these algae end up controlling them. They’re very silly.
Castes in eusocial bees are raised differently, under different ambient conditions (temperature, humidity) and given different types of food. For the future queens, the larvae are fed with this special mixture called royal jelly, the secret component of which are major royal jelly proteins. These are the active component that cause the adult queen phenotype to emerge after metamorphosis. This paper contributes some intriguing information about bumblebee major royal jelly proteins that has implications for how we think of the evolution of this system.
For more on the evolution of these things, see Drapeau et al. (2006).
For all their intelligence, salticids do have a stereotypical atttack pattern. They detect their prey with their peripheral vision, turn towards it and start tracking it with their principal eyes. They move stealthily towards it with a characteristic posture, and jump on it when within 3 cm. This paper shows that there is age-related variation in this stereotypical pattern.
You’ve all noticed that if you try to grab a spider by the leg, it will cut it off – a process called autotomy (see here for information the regeneration of the lost limb). This paper states the obvious: missing a limb will have a negative effect on the speed of spiders (it’s nice to have concrete numbers though!).
Apparently, female dytiscids exhibit different morphologies. There can be grooved and smooth elyra forms. This study is a straightforward Mendelian one, except the peas are replaced with dytiscid females, and the trait examined is the elytral sculpture (grooved vs. smooth). It turns out that it’s all genetically determined. I’m not sure of the generation time of dytiscids, but if it’s short enough, this would be a neat way to let students derive genetic inheritance patterns by themselves as a lab project.
This is a simple primer on the microbiology of cheese. I’m not into microbiology, biotechnology, and the only cheeses I like are those that are melted in a sandwich or pizza, but this is good party trivia.
There are two points in this paper. One is phylogenetic methodology, and the other is about land plants. The former concerns the importance of checking the data that you input into your molecular analysis. It’s no use just blindly sequencing and downloading data and running through a prefabricated checklist. That’s not how phylogenies are reconstructed, and it’s what leads to bad results. This paper demonstrates the importance of making sure your input data is solid, using the origin of land plants as a case study.
For more on the origin of land plants, see this post, Steemans et al. (2009), and McCourt et al. (2004).
- Patterns of comb row development in young and adult stages of the ctenophores Mnemiopsis leidyi and Pleurobrachia pileus.
I was attracted to this paper by the last sentence of the abstract:
The different modes of comb plate formation in Mnemiopsis versus Pleurobrachia are accounted for by differences in mesogleal firmness and mechanisms of ciliary coordination.
I’ve always thought that developmental biology needs a lot more focus on physical and mechanical forces acting on the embryo, instead of just looking at genetic and molecular cascades. As a non-developmental biologist, I’m not in any position to say hopw much research is conducted on those mechanical aspects, but it doesn’t seem like much. This paper shows that there is reason to study it though.
This is a review of both the development of those respiratory systems, as well as of branching morphogenesis, a type of morphogenesis implicated in the formation of all sorts of epithelia (and the mammalian kidney). Well worth keeping.
This is an evo-devo paper, concentrating on the developmental novelty present in holothuroids: a larval skeleton, not found in other echinoderms. If you’re interested in evo-devo and the origin of evolutionary novelties, read this.
For a general look at holothuroid evo-devo, see Kerr & Kim (1999).
Kick sampling and the Hester-Dendy are two ways of sampling stream and river biodiversity. Kick sampling is basically kicking the sediment at the bottom of a river, and setting up a net a bit further downstream to catch whatever animals get disturbed. A Hester-Dendy is basically a plate left on the sediment for a period of time during which it gets colonised by the animals living in the stream. Pick it up and collect the beasts. This paper quantifies the differences between the two methods – it’s important to choose the right method for your study, after all.
This paper quantifies the diversity of tree-dwelling ants in a primary forest and a secondary forest. It’s well-known that secondary forests harbour less diversity (something that can be said of most anthropogenically-prepared habitats, e.g. artificial reefs), and this study comes to the conclusion that the reason is that the habitat structure is too simple in secondary forests, compared with the natural primary forest.
- Temperate and tropical brown macroalgae thrive, despite decalcification, along natural CO2 gradients.
This study is about phaeophytes (calcified brown algae) and sea urchins growing near volcanic seeps, which constantly release CO2 into the surrounding waters and thus act as great natural laboratories for seeing the ecological effects of increasing levels of ocean acidification (near the seep = highest acidification; levels drop as you go away). The study is conducted in the tropics (Papua New Guinea) and in the Mediterranean, and the results were similar in both cases (meaning they can be generalised to a certain extent): sea urchin concentrations decrease in more acidified waters, while some of the phaeophytes bloom despite being decalcified, because they don’t get eaten by the sea urchins.
- Segment number, body length, and latitude in geophilomorph centipedes: a ‘converse-Bergmann’ pattern.
Bergmann’s rule basically states that larger ectotherms are found in colder climates than in warmer climates. The debate on the validity of this pattern has been going on since it was proposed by Bergmann (1847). This paper contributes a a data point invalidating it in the case of geophilomorphs.
The literature on Bergmann’s Rule is quite extensive. See Meiri (2011) and Meiri & Dayan (2003).
- Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation.
This is a study on speciation in Nebria carabid beetles, specifically related with altitude – the basalmost species, Nebria ingens, is also the one found at the highest levels of the mountains in the Sierra Nevada, and they gradually get younger as you go down the mountain, as would be expected from a Pleistocene species pump model, where the Ice Ages and associated climate changes caused increased speciation.
Niche models are models of what environmental conditions a species can tolerate, and are therefore used to predict how species will react to climate change, how they will act as invasives/against invasive pressure, and other such information. They’ve recently come under flak (I’m not an ecologist, so I can’t describe the details of this), and this paper does a good job of defending the practice.
Like I mentioned in 5. above, the Ice Ages had an effect on speciation. This is further demonstrated in this paper, where it’s shown that Australian freshwater populations got pushed there by the climate changes (Australia became a glacial refugium, where species could hide away from the glaciers), and subsequently radiated.
A big thing in ecology is to find biologically meaningful ways to categorise communities. This paper demonstrates the validity of such an approach.
It’s no secret that one of the great injustices of our current environmental crises is that those crises are predominantly caused by developed countries who should know better and certainly can do better, and those worst affected are poor, developing countries who have no choice but to suffer at the idiotic hands of the rich countries. This paper models the whole thing, finding that developed countries contributed between 60-80% to our current climate debacle, and suggests how recovery actions should be split among countries.
For those of you concerned with what we can do to keep our current extinction rate in check, read this paper. I’ll let the abstract do the talking:
Our analysis suggests three globally relevant recommendations for minimizing species extinction worldwide: (1) informed, empowered, and responsive governance and leadership is essential; (2) processes that ensure institutional accountability must be in place, and; (3) decisions must be made whilst there is an opportunity to act.
Considering that poalr bears live on sea ice, it’s obvious that as the climate warms and that sea ice melts away, they will be placed under ecological stress. This paper summarises the stages polar bear populations will go through as the climate warms.
Polar bears are cold-climate animals, but some butterflies are adapted to warm climates. Intuitively, one would hypothesise that those warmth lovers would benefit from global warming. Not so, says this research.
Ocean acidification is seen as a large problem because the acidity destroys the calcareous shells of many ecologically important organisms. Among them are the coralline algae, and this study gives details on how the acidity affects the calcareous skeleton, and its implications.
For more on the effect of ocean acidification on coralline algae, see Kuffner et al. (2007). For its effect on the carbonate balance of the oceans, see Feely et al. (2004).
It’s no secret that conservation biology deals a lot with charismatic animals. Pandas, tropical birds, penguines, polar bears, butterflies, these are all animals whose perceived cuteness dictates that their image be exploited to get funding and public support for conservation efforts. This paper brings up flowers and their colour as another component of diversity that has to be conserved, as flowers and their colours have cultural significance. It’s the same kind of thing, although one can also make a very valid argument for flower colour needing to get conserved because of their interactions with polinators.
So there is no consistent definition of the term “species” used by all biologists. The biological species concept is the most common one, but it’s not really tested in most taxonomy. The phylogenetic species concept (the one I subscribe to) makes stability a nightmare to achieve. And so on for all the rest of them. This paper deals specifically with what they have to say about conservation biology.
- The response of life-history traits to a new species in the community: a story of Drosophila parasitoids from the Rhône and Saône valleys.
If you’re interested in the impact of “invasive” species, check this paper out.
Polyommatus icarus is the common blue butterfly (or so it’s called in the UK). This study shows that they’ve experienced a bottleneck in the UK, which has implications for conservation (not that it’s endangered anyway).
Taxonomy is probably the most unfunded science around, relative to importance. It’s the foundationals cience of biology, the science that allows us to discover the biodiversity which all other fields of biology use for their studies. But it gets very, very little money for all the raw information it gives back. In any case, read this paper to find out why taxonomy should be funded, in case you have doubts. Everything described in the paper falls under its wing.
See Agnarsson & Kuntner (2007) for more on the whole taxonomy crisis.
One of the effects of climate change on the biosphere is that it will influence phenologies of plants – when they will bloom, regain their leaves, etc. This obviously has knock-on effects on the rest of the ecosystem, and so understanding how phenologies will be affected precisely is an important field of study. This study contributes some hard data.
It doesn’t take much to get taxonomists and systematists riled up – argumentation is one of the key skills you learn when becoming a taxonomist or a systematist, because the only way to survive is to know how to state your case properly. Few papers have gotten such a reactionary response as this one though (a simple search through my inbox for “costello et al” turns up a bunch of not so pleasant e-mails). And it’s not hard to see why it got such a negative press – the assumption that the rate of taxon discovery is correlated with total number of species is sketchy. Too many flaws can be brought up. To the credit of the paper, the data on species discovery rates is useful. It’s just the jump from discovery rate to total expected number of species that’s dreadful.
The paper estimates 1.8-2 million species. The more mainstream estimates are in the ballpark of 10-12 million.
With all the talks of extinction crises nowadays, it’s nice to see species thought to be extinct suddenly reappearing. These crop up every once in a while (Scottish polecat, clivinine beetle, hadenine… the list goes on). For a critical look at the meaning of such rediscoveries, see Crowley (2011).
I place this under Evolution and not arthropods because it’s a striking example of convergent evolution at the molecular level. Convergence at the morphological level can intuitively be seen as easy to evolve – it’s easy to see the same functions being achieved by similar morphologies. In this paper, the same principle is shown at the molecular level: 18 species from four insect orders have convergently come to the same solution to cardenolide resistance. It’s pretty cool, and I will be using this as a staple example in future evolution lectures.
For another excellent example of convergence at the molecular level, see Rosenblum et al. (2010); I describe it in this post (search for “White Sands”).
Along with islands, caves are one of the iconic realms where evolution can be studied to get great, paradigmatic results. This paper reviews the evidence about processes taking place in subterranean environments, coming to the conclusion that absence of light, competition, and taxon age are the most important factors in cave evolution.
For examples of how caves are awesome model environments for the study of evolution, see Jeffery (2008).
This is a very interesting paper, as the title should clue you in. It’s no secret that many animals can learn (some would say it’s a natural consequence of having a centralised nervous system), so obviously this will play a role in the life history of the animals, and subsequently affect their evolution. This paper reviews the different ways how learning interacts to influence mate choice, and so how it influences sexual selection and, eventually, speciation.
Nothing much to say here. If you work in the Late Triassic, you might want to save this paper. For more on Triassic stratigraphy, see Lucas (2010).
The P-T extinction was the largest mass extinction event of all time, and was caused by superanoxia in the oceans, combined with ocean acidification and massive climate changes. This paper gives more geochemical data on the former two aspects.
See the end of this post for a summary of the causes of the P-T extinction.
Few things are cooler than seeing the holographic 3D projections of regional geology that oil companies can produce to know precisely where and how to drill. This isn’t science fiction, it’s real. Albeit outside the scope of most geologists. But regular 3D modelling is a matter of GIS. This paper reviews it.
The Mid-Pleistocene Climate Transition occurred 900 ka, and was when Earth’s climate changes became predominantly modulated by orbital eccentricity (the 100 ka cycle of the Milankovitch Cycles). Why this suddenly happened is still a mystery. The main result to take away from this paper is that climate changes tend to be pretty abrupt. “We see no evidence of a pattern of gradual cooling, but near-freezing temperatures occur at every glacial maximum,” as the abstract says.
Those interested in the intersection between science and art would do well to read this paper, because it raises the issue that the scientist who wants to also do art has to work towards finding new methods to portray what he’s seeing. So to apply it to nowadays, maybe the next step beyond CTs and ultra-macro stack images is 4D holograms. Or something.
You can read Micrographia at the BHL. Check it out.
The title is self-explanatory: the authors describe the up-to-now basalmost snake known, Coniophis precedens, on the basis of newly-discovered material. No need to go through the details. The most important part of this is that it confirms the importance of the kinetic skulls of snakes, described in this post. Coniophis‘s skull was akinetic, very similar to the head of a regular lizard. It was only after the bodily habitus of snakes evolved that the kinetic skull also evolved, along with their specialised ecology. This could be used in a classroom as a case study for the interaction between functional morphology and ecological evolution.
Species of new human species, so of course it’s an immediate Nature paper (you can send them a manuscript of new human species written on a napkin and they’ll print it). Anyway. Yeah, two new early Homo species. If you’re into this stuff, I guess you’ll find it exciting.
See Tattersall & Schwartz (2009) for a (slightly outdated, obviously) review of the evolution of Homo.
The Carboniferous is known as the time of the great coal swamps. This study analyses the diversity of the plants that made up these forests and finds that the biodiversity was low. Despite this, the ecosystems were fairly hardy and remained static for quite some time.
The Yanjiahe Biota isn’t one of the iconic Cambrian Konservat-Lagerstätten, but it’s still worth studying. It’s a sandy/cherty dolostone formation with some limestone and black shale beds, deposited in the early Cambrian (it overlies Dengying). Most of the fossils there are microscopic acritarchs and small shellies, but now an enigmatic putative stem echinoderm has been found from there, as described in this paper. This is an addition to the already wonky early evolution of echinoderms – at the time, they had very little in common with today’s depauperate echinoderm fauna.
See Smith (2005) for a summary of these weirdo Cambrian echinoderms.
I often refer to Cambrian animals as “freaks” and of that time of animal evolution as a period of wacky experimentation (see here). This is overembellishment and is constantly being shown as not true. The view used to be supported by the fatc that no Cambrian animals were known past the Cambrian – it was thought that there was an end-Cambrian extinction. However, this view is gradually losing support. With the finding of Devonian anomalocarids and marellomorphs, it became clear that the “extinction” is probably nothing more than a fossil record bias, caused by the sparseness of Konservat Lagerstätten compared to the Cambrian. Some more nails for the coffin are presented in this paper, which presents the finding of a new Carboniferous long-legged lobopod, extending their fossil record by a staggering 200 million years (even though they’re not a monophyletic group, they’re treated the same because of it’s the best consensus to take).
See Liu et al. (2008) for more on lobopods.
- A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times.
- The Relationship between Genus Richness and Geographic Area in Late Cretaceous Marine Biotas: Epicontinental Sea versus Open-Ocean-Facing Settings.
There’s not much to say here, except a personal note that I love this new wave of sophisticated geographical studies on the ancient ranges of organisms. I am learning the ropes and will be applying these same methods for my own palaeontological research in Cyprus.
For those interested in delimiting species, species concepts, and the associated messes. This paper roughly describes my own views, that we have to look at species holistically. In other words, the only way to delimit them is to look at their evolutionary history, not just to see whether they interbreed or not.
It sould come as no surprise that I’m a supporter of the PhyloCode. Some may laugh and mock, some may admire the persistence, and some will be thankful for the support. Whatever. I think it’s a great idea to change the nomenclatoral system to reflect proper evolutionary biology. Anyway, read this paper for more and more perspectives.
For more on the PhyloCode, see Dayrat et al. (2008). For a critical look, Benton (2007; warning PDF) does the trick.
- Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny.
- The Probability of Correctly Resolving a Split as an Experimental Design Criterion in Phylogenetics.
There are two types of bat echolocation, LDC (low duty cycle) and HDC (high duty cycle). From the abstract:
Most echolocators (most bats and all birds and odontocete cetaceans) use LDC echolocation, separating pulse and echo in time to avoid forward masking. They emit short duration, broadband, downward frequency modulated (FM) signals separated by relatively long periods of silence. In contrast, bats using HDC echolocation emit long duration, narrowband calls dominated by a single constant frequency (CF) separated by relatively short periods of silence.
This paper analyses the advantages and disadvantages of HDC echolocation to see how such a mode can evolve.
For more on the evolution of bat echolocation, see Speakman (2001).
- Unusual pattern of embryogenesis of Caryophyllia inornata (Scleractinia, Caryophylliidae) in the Mediterranean Sea: Maybe agamic reproduction?
If you’re interested in coral reproduction.
Marine organisms are where future research into finding new drugs will be conducted. From the defensive cocktails of sponges to those of corals, there’s plenty of potential for new compounds to be found. Step one of such research is characterising the chemical diversity of the secretions of a species. But until this can be measured directly, one can do like in this paper and just check the genetic diversity of defensive glands. It’s not in the context of drug-finding, but one can coopt the method.
Would you be able to indicate which papers are open access and which are not in future? This is a great list by the way. I’ll be on the look out for another!
Okay, I’ll make them easier to spot int he future by adding an [OA] tag in front of them, easy to find with Ctrl+F. Thanks for the feedback ^^
I was on my phone traveling and fancied some good reading. I was just being a pedantic really. Thanks for the reply and keep it up!