Papers of the Week

19 08 2012

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.

60 papers this week, 8 special issues. Breakdown below.

Index:

Special Issues:

A special issue on various aspects of barnacles, including their biology, phylogeny, and economic importance. I wrote a post on barnacles if you want basic background information. I found the following papers particularly interesting: Høeg et al. [OA] on metamorphosis, Holm on biofouling, Yamaguchi et al. on their sexual diversity, Ewers & Wares on their molecular peculiarities, and Pérez-Losada et al. [imp] have a thorough thecostracan phylogeny.

I can’t really say I enjoy this field, but some readers may be interested in cell biology or biochemistry. For my part, I only read Hunter‘s paper on what makes phopshorylation so successful.

Scroll down to the end to get to the special section, which has papers on medicine in the 1700s in Central Europe. I found Krász and Bräunlein interesting, mostly because of the titles (quacks and vampires, awesomeness).

Nature‘s latest Insight series is about renewable energy. All papers are open access and pretty good summaries of the state of the art.

A special issue on how to manage the now-massively developing countries onto a more sustainable path. It’s mostly cenetered on China. The paper by Sugar et al. is a good summary of how muchgreenhouse gases several large Chiense cities emit.

I get mixed feelings from colleagues about meta-analyses. Half like them, half don’t. I personally like them, even if they do have their drawbacks. This is a good series of papers about meta-analyses and their applications in ecology, it should be useful in persuading the naysayers.

For those interested in this stuff. I only looked at Minegishi et al. [OA].

Arthropods:

Everyone knows how the females in nesting birds leave their offspring to get food, and come back to feed them one by one. Many animals do something similar; mammals are the big exception since they have boobs to feed their children with. In this paper, a shield bug that provides its offspring with food has been found to emit a special call to gather the kids to the food once it gets back to the nest. It’s the first time I hear of such a strategy. The authors give it a new name, provisioning call.

Examples of parental care in the insect world come a dime a dozen. Field et al. (2007) examine it in digger wasps for a random one.

This study is pretty huge. I can’t imagine how logistically difficult it must have been to track a thousand hermit crabs and their housing changes, so kudos for the effort. The results are also pretty cool, showing that hermit crabs don’t just pick random objects to use as shells, but actively seek out appropriate objects and even modify them to make them nicer to live in.

Altitudinal gradients are very cool to study; you can check the intro and discussion in my recent paper for many reasons. This paper shows how an altitudinal gradient and the associated ecological differences can lead to isolation and the beginnings of speciation in a ground beetle species.

This is just an excuse for necrophilia.

Apparently, if you deprive male locusts of females, they form homosexual orgies. It must be an awesome sight to behold. Anyway, this paper clarifies the neurological basis for their homosexuality – it’s controlled, or at least enhanced, by juvenile hormone.

In case you’re wondering, homosexuality is present all across the animal kingdom. It’s nothing special. Here’s a couple of random papers with gay insects: Levan et al. (2009), Maklakov & Bonduriansky (2009), McLachlan (2011). See also Poiani’s 2010 book, Animal Homosexuality: A Biosocial Perspective, for a comprehensive overview of homosexuality.

This stuff is way outside my knowledge field. It’s about the relationship between insect photoreception and circadian rhythms. Check Koštál (2011) and Yuan et al. (2007) if you’re interested in more.

Some more confusion for the hymenopteran tree: this molecular analysis finds that the Apoidea (the group that contains the bees) is actually within the Crabronidae, as opposed to its sister group. See Sharkey (2007) [PDF!] for an overview of hymenopteran phylogeny.

For another phylogeny of oedipodines, see Fries et al. (2007). A good project assignment for students learning bioinformatics or phylogenetics is to give them different phylogenies and have them plot the same character set on them, and see what different conclusions about evolution can be drawn. It can eb done with this wing morphology stuff in oedipodines, for example. It not only teaches the technical aspect, but also how to properly treat phylogenies as a source of evolutionary information.

The Culicini tribe contains one of the “iconic” mosquito genera, Culex (the other is Aedes, not in the Culicini). See Harzbach (2007) [PDF!] for more on mosquito classification and phylogeny.

Butterfly wing patterns are a classic model system for evo-devo. Everything from their development to their retention and modification by natural selection, and the interactions between these two fields, can be investigated. Case in point, this paper finds that eyespots evolved only once in nymphalids (emperors, admirals, fritillaries…), and their subsequent evolution can be traced using gene expression patterns.

For more on evo-devo and butterfly eyespots, see Monteiro (2008).

Aphids are some of the most annoyingly (fascinatingly?) polymorphic animals. They don’t only vary drastically by sex, but also by life cycle and generation. I personally can’t stand them and avoid working with them as often as possible, and I recommend all others to do the same, unless you don’t want your sanity. Anyway, this paper gives some information on how different the flight system is betweent he males and females in this species, finding that the males and females and nymphs have all been under different selective pressures to produce such a wide array of wing morphs, from male flightlessness to winged females.

For more on wing variations in aphids, see Braendle et al. (2005), Braendle et al. (2006), and Brisson (2010).

There are some gorgeous pictures to be seen here. It’s an atlas of spiracular morphology in all scolopendromorph families, and there’s a useful character matrix.

Cuticular hydrocarbons are compounds that cover the cuticle of an ant. They’re individual- (or at least caste-) specific. Ants touch each other with their antennae and detect these hydrocarbons to recognise each other. This paper shows that they can even recognise the fertility of fellow ants (something useful for policing, since only the queen is supposed to be fertile).

For more on ant recognition, see Sturgis & Gordon (2012) [PDF!], and Nehring et al. (2010).

Some more on how ants can differ even in the same caste. I like to show these papers around just so that people stop thinking of ants as armies of preprogrammed clones with no differences between them. (Granted, this is a paper about queens, but the same can be found in workers and soldiers.)

Biochemistry:

I wonder how much of the apparently well-developed ability of photosynthetic organisms to survive anaerobically (outlined in this paper) traces back to the time lag between the evolution of photosynthesis and the Great Oxidation Event, when the organisms were essentially living in anaerobic conditions.

Botany:

Orchids are famous for their risky method of pollination. They deceive male insects into thinking that the flower is a female, and the male insect goes on to try and copulate with the flower (it’s called pseudocopulation). The way the orchids do this deception is either visually – the flower looks like a female to an insect (insects usually discriminate only shapes and silhouettes and colour patterns, it’s not that hard to do a visual trick) – or by scent (mimicking a sex pheromone is the usual way). This paper examines the genetic background of how three Ophrys orchids manae to make a blend of chemicals to mimic the sex pheromones of their pollinators.

For more on Ophrys chemical sexual deception, see Schiestl et al. (2000), Ayasse et al. (2003), and Schiestl et al. (2003).

Developmental:

Ecology:

This paper finds a surprising pattern: that in the marine realm, the highest biodiversity isn’t found in the Equator (as it is in the terrestrial realm), but 10-20° north and south of it (exact breakdown in the paper). Reasons for this proposed, from the abstract:

Possible explanations may include a coincidence with the intertropical convergence zone, a mid-domain effect, abundant shallow marine habitat, or high ocean temperatures at latitudes nearest the equator.

I find this result interesting because a similar effect can be seen in terrestrial altitudinal patterns. As background, altitudinal gradients are often used as substitutes for latitudinal ones when considering broad abiotic factors (see the intro and discussion of my recent paper). And in terretsrial altitudinal gradients, we also often observe a pattern of peak diversity after 200 m instead of right at the bottom. This is my own crazy talk, but maybe one could try looking for a general link between these two patterns. It may be coincidence, or it may be that there really is some effect that generalises to mid-elevation or mid-latitude or post-0-level peak diversity. Probably just crazy talk though.

I am thinking of doing a similar study in Cyprus once the wet season starts again. Maybe not with caddisflies. Anyway, this paper is worth reading even if you’re not interested in Mediterranean ecology, because it highlights how looking at things from diffferent scales gives you completely different information. This is something that applies not only to ecology, but to all the biological sciences. One has to be very careful to make sure the scale of your testing corresponds to your hypothesis.

This is something that’s interesting to me since half my research is about endemics on an oceanic island.

Anyone working in freshwaters has to have this paper.

If I ever bother updating the My Research tab, you’d see that one of my main research projects involves vernal ponds, and my main personal objective is to elucidate exactly what’s being talked about in this paper (personal objective, because the project is more general, I just like to concentrate on the evolutionary side of things rather than the ecological stuff).

Environmental:

I often, surprisingly in this day and age, get asked about whether it’s true that people from other “races” are less intelligent than Western white people. My ideal answer would be to drop Western white people in the Amazon and watch them promptly die, then go hang out with the indigenous tribespeople who are smart enough to know how to survive in that environment. Point of the story is that not only is intelligence not a trait that’s universally measurable (and hence it’s a pointless thing to ask), but also that locals are always more knowledgeable than anyone else on their area. Those Amazonians I am hanging out with can identify on sight and sound more species of animal and plant than I even know the names of, as well as tell me their ecological preferences.

How does this rant relate to this paper? This paper’s about how to properly integrate and link local people’s knowledge about their environment to our science, something that’s pretty important to do (it’s done more and more in conservation and ecology).

Last week’s issue from the Philosophical Transactions of the Royal Society A was on geongeineering. This paper can be added to those ones – it’s about how the public looks at geonengineering, important to know in these days of widespread conspiracy theorising about Big Evil Science. For my personal take, I think most geoengineering schemes are poppycock that might ultimately do more damage than good, so it’s best not to risk it. This includes things like seeding the oceans with iron, using aerosols to brighten clouds, and other large-scale engineering projects. I don’t mind small, local ones (expanding peatlands and swamps, etc.). But this is all personal, and not expert, opinion.

All you need to know about Greenland’s climate history, current trends it’s experiencing, and their potential impacts.

There is nothing I hate more than getting in a debate with a climate “skeptic”. These are idiotic to the same level as the paragons of idiocy, i.e. homeopaths and creationists. I just thought I’d share, because I can’t really say anything about this paper. I don’t understand this communication stuff.

When I first started involving myself in environmentalism and climate change, I figured that the domestic section of energy use and emissions is negligible. After all, what are houses compared to enormous factories and industrial estates? Turns out I was wrong. In the average industrialised country, domestic energy use and emissions account for a third of them, so there are tangible benefits to be gained from cleaning up household consumption (besides feel-good uselessness). This paper is about the factors standing in the way of greening the housegold, from the human and economic sides.

I include this in the environmental section because population control is one of the most pressing issues that needs to be dealt with if we’re ever going to have a hope of living sustainably past this century. It’s always good to learn from the mistakes of the past.

Evolution:

Climate change is obviously having a drastic effect on the biosphere, but the evolutionary effects of it still need to be investiggated thoroughly. How much will organismal survival depend on de novo adaptation and thus natural selection, and how much will be taken care of ecologically through range shifts or through plasticity? This paper explores these questions.

I recently gave a talk on this stuff. I wish this thorough review had come out sooner so I could have plagiarised it all and spared myself a whole load of work.

Geology:

The Snowball Earth period, 750-580 Ma, was one of the coldest periods in the history of life on Earth. At one point, it was thought that ice reached all the way to the Equator (hence the name); this is now considered unlikely, but the extent of the time’s glaciations has never been seen again. This paper examines how the lower ozone levels of the time contributed to the cold – ozone is a greenhouse gas, so it stands to reason that lower ozone levels would have reinforced the coldness trend; the paper overwhelmingly confirms this.

For more on the Snowball Earth, you can check the original paper by Hoffman (1998) and a review by Hoffman & Schrag (2002). Kopp et al. (2005) [OA] is also good reading.

The Late Miocene saw the emergence of a warm, tropical climate – basically, like the climates of today, but warmer and with more precipitation. There were grasslands were now there are deserts, and there were lush forests where now there is tundra. As such, it’s an interesting time of Earth’s history to study, to see if maybe, just maybe, this is the direction our current global warming is shooting us towards. Chances are that it’s not, but it would be nice. This paper’s about technicalities I don’t fully understand anyway, but it does have a good introduction.

For more on the Late Miocene climate, see Bruch et al. (2004) and Böhme et al. (2008).

History of Science:

Despite the claims of creationists worldwide, Darwin isn’t an idol to be worshipped. In fact, for all the he got right, he got as many things wrong, and much of his research is now outdated (so much so that I don’t even recommend reading The Origin except for literary value and scientific method value). One of the things he got wrong, as demonstrated in this paper, is his strange stance on sexual selection in humans, outlined in The Descent of Man. He really fell off the deep end in these sections, drawing unevidenced conclusions everywhere (much as modern evolutionary psychologists do with their fantastical concept of evolution). It’s just a muddled mess, and it’s nice to see it get taken down.

You can check my post on Darwin for a level view of the man and his achievements.

Microbiology:

Microbialites are sediments produced by microbial processes. The most famous are stromatolites, carbonate mounds with layers produced by cyanobacterial colonies. This paper reviews the cyanobacterial composition of several microbialites from different ponds in Yellowstone.

Palaeontology:

The Kellwasser and Hangenberg events in the Late Devonian were some of the most severe extinction events in the history of life. However, it’s long been realised that the Devonian was a time of lots of smalle xtinctions, and referring to these as “events” is a bit disingenuous, since they were more probably collections of events. This paper presented evidence, in the form of cyanobacterial mats, that there indeed wasn’t one massive event, but that this was a very dynamic time, with lots of changes happening quickly.

Another example of fossil record bias acting up, a topic I wrote on before in this post.

Phylogenetics:

There are three hypotheses about where humans stand with respect to the other apes. The predominantly established view is that humans and chimps clade together; this is supported all around. There’s another possibility, that chimps and gorillas clade together, with humans as their sister group; this can be supported using phylogenomics. The third, and most disregarded, is the view that humans and orangutans are sisters, supported by a highly-selective number of characters. This paper critiques two analyses done to support this latter view, and in doing so provides an excellenet showcase for how to criticise phylogenetic analyses.

The critiqued papers are: Grehan & Schwartz (2009) and Grehan & Schwartz (2011) [OA]. Read them with a pile of salt. Personally, I couldn’t care less about ape relationships. I do find the gorilla+chimp clade interesting since it’s supported by phylogenomics, but I will go with the consensus flow since I know nothing about this neighbourhood of the animal kingdom.

I include this in the phylogenetics section because I don’t deal with Carribean geology, and I’d like to comment on why I was even attracted to this paper. The use of phylogenetic methodology in fields other than systematics is something that’s of great interest to me. Linguists do it all the time. I myself have had two semi-successful attempts at applying it to classifying moral and social structures, as well as to creation myths. IU never thought of applying it to geology as in this paper, but this has intrigued me a lot and I will now be looking into it.

Zoology:

This paper takes a look at the evolution of flight in bats from an evo-devo perspective. See Speakman (2001) for a more general look at the evolution of flight in mammals.

The extraxial-axial theory is one of the more exciting developments in evo-devo. It allows us to look at echinoderms in a completely new light, combining evolution and developmental biology to clarify the morphology of what has always been a mindfuck taxon, due to the echinoderms’ earliest representatives not being pentaradially symmetric. All modern echinos are pentardially-symmetric, but this is a derived condition that doesn’t allow us to compare them directly to their fossil record. The EAT allows us to do so by looking at how everything develops before the pentaradial symmetry overprints everything.

See Mooi & David (2000) [OA] for more on the EAT.

Those interested in animal behaviour and neuroethology should get this paper. For a similar paper on vocalisations specifically related to food, see Clay et al. (2012).

I don’t care much for bat brains, but this is a cool demonstration of the use of advanced technology in palaeontology – they used tomography to measure the brain size of fossil bats.

The problem with the term “living fossil”, besides the fact that fossils can’t be living by definition, is that it automatically confuses. What exactly is a living fossil? In a way, all living organisms are living fossils since they all have descendants from the fossil record. Current sponge morphotypes are all found in the fossil record, so are all sponges living fossils? The commonly cited living fossils (monoplacophorans, coelacanths, crinoids) are all animals that were thought extinct but get rediscovered. There’s actually nothing spectacular about them. Their fossil record just gets extended, that’s all. It’s only something special if we find out that they have actually retained the exact same morphology for millions of years, because that hints at unique macroevolutionary processes happening to retain such morphological conservatism. Or, their morphological conservatism may simply be due to developmental or phylogenetic constraints – they can’t change their appearance so much. Or, it’s all convergent. Lumping everything as living fossils, while nice for the public, is not conducive to good science. Anyway, this rant is only tangentially relevant to the paper.

For more on monoplacophorans, see Lindberg (2009).

Ascidians are cool study systems because they have a large diversity of life cycles, from solitary to colonial forms. Colonies get propagated by budding, but the details vary in each group, meaning there’s a lot to be studied here in terms of how these various life cycles and strategies have evolved. This paper reviews how stem cells are the cause of all this variety.

For more on the importance of stem cells in colonial ascidians, see Laird et al. (2005). For more on colonial growth by budding, see Kürn et al. (2011) [OA].

If you want to be fascinated by miniaturisation, look no further than crustacean plankton. These are organisms that are invisible to the naked eye, but still packing complete complete organ systems as known from their larger counterparts, including fully-functional brains. Puts our human inefficient mess to shame. This paper examines the brain of a copepod. If you’re interested in copepods or in arthropod phylogeny, get it.

Lacalli (2009) looks at parts of the brain of a larval copepod.

Some more examples of marine fungi.

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26 08 2012
The Week on Sunday | Splendour Awaits (15:11:54) :

[...] Srour, an invertebrate palaeontologist, blogs over at Teaching Biology. Weekly, he posts some of new scientific papers that manage to pique his interest. And I, like a [...]

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