Papers of the Week: 30.04 – 05.05.2013

Papers from this week. [OA] indicates open access, and all are discussable on request.

General Interest, Important:

• Charles Darwin’s Mitochondria. [OA]

After he came back from the Beagle voyage, Darwin never set foot on a boat again, and he became a sort of recluse, using a mysterious illness as an excuse to avoid excessive socialising. Opinion has generally been split between him suffering from Chagas Disease, or him merely being a hypochondriac. This paper proposes another hypothesis, that he was suffering from some sort of mitochondrial disease, based on analysis of his maternal family tree: several of his maternal family members died of mitochondrially-caused illnesses, so it was likely he had some sort of mitochondrial dysfunction as well.

• How to get into bones: proton pump and carbonic anhydrase in Osedax boneworms.

I mentioned Osedax back in the very early history of the blog in one of the deep sea posts. They’re fascinating little creatures, a specialised genus from an already highly-specialised annelid family that lives only in extreme marine habitats, have no mouth gut, or anus: the Siboglinidae. They feed by having chemoautotrophic endosymbionts in them, with the only exception being Osedax, a genus first described only in 2004. The Osedax female burrows its hind end into bones that have fallen on the ocean floor, and then branches out into the bone, like a root system. Inside a special organ called the trophosome lie a bunch of gamma-proteobacterial endosymbionts which digest the bone and hand the nutrients off to the mothership. This paper greatly expands our knowledge of this system, by finding that the roots help the bacteria by mass-producing acid to help dissolve the bone, allowing the roots to spread further, and the bacteria to have easier access to bone.

• Increased morphological asymmetry, evolvability and plasticity in human brain evolution.

Some more data on the plasticity of the human brain. It’s a pet topic of mine, since I often cross swords with people who think that intelligence is completely genetically hardwired into every individual human, thus throwing away everything we know about the evolutionary history of humans, all of social science, and quite a bit of evolutionary theory too.

• Triassic–Jurassic mass extinction as trigger for the Mesozoic radiation of crocodylomorphs.

I summerised what happened to vertebrates at the end-Triassic in a single slide in my Mesozoic Vertebrates lecture. All the Crurotarsi died out, except for one group, the crocodylomorphs. This paper provides a much higher resolution of what happened to the Crurotarsi. Yes, all but the crocodylomorphs got wiped out, but there was no significant shift in disparity – which means that the crocodylomorphs must have had an incredibly quick and effect adaptive radiation to replace all the other ecotypes.

• Production of chimeras between the Chinese soft-shelled turtle and Peking duck through transfer of early blastoderm cells.

Just something to freak out those who think that science has gone too far: turtleducks! Frankenstein’s Monster is just one day away! Okay, not really, there was no phenotypic change, but this is very cool nonetheless, showing that cells from two different classes can get developmentally integrated into the adult, at least in the case of duck cells in the adult turtle.

• Controlled Flight of a Biologically Inspired, Insect-Scale Robot.

Bioinspired robotics are pretty awesome, and one of the best practical uses of zoology and especially entomology – the modular design of arthropods and insects is very conducive to engineering. I’ve written about insect flight and its complications here and here, and this paper demonstrates a robot that has replicated it. Impressive.

• The insect molecular clock.

The molecular clock is another one of my pet topics, with my preferred scientific hobby being to shit on the majority of molecular clock studies. See my beef with it in this four-part series: 1, 2, 3, 4. This paper critically discusses molecular clock applications in insects.

• Alleged silk spigots on tarantula feet: Electron microscopy reveals sensory innervation, no silk.

The presence of silk-spinning spigots (see my spider lecture) on tarantula feet has been one of the recent controversies of tarantula biology. This could be the death knell for this story: tarantulas have weird stuff happening in their tarsi, but silk-spinning isn’t one of them.

• Misconceptions of sexual selection and species recognition: a response to Knell et al. and to Mendelson and Shaw.

A very interesting exchange happening in TrEE on how sound studies asserting the presence of fossil sexual selection and sexual dimorphism are. Be sure to read the replies by Knell et al. and Mendelson & Shaw. There are valid points raised by all parties.

• Special Issue: Nuclear Energy Models and Strategies.

Like any reasonable environmentalist, I’m a fan and supporter of increased nuclear power. Of course, the irrational public perception and fear of nuclear power is one of the larger impediments. The papers here are level-headed and show that nuclear power must be a key transitional power source to wean us off of fossil fuels.

Papers of the Week: 22.04 – 29.04.2013

Papers from the past week. [OA] are open access. Feel free to request a detailed discussion on any of these.

General Interest, Important:

• Special Issue: Vivisection

Vivisection, the practice of dissecting living organisms for scientific study, is nowadays mostly frowned upon for bioethical reasons. We can study anatomy when the animal is dead, and there are many technologies available to allow us to non-invasively study physiological systems, so there is no major reason to do vivisections anymore. These technologies haven’t always been here though, and a lot of the early biological sciences were filled with accounts of vivisections, which did bring about a wealth of knowledge, so they weren’t wasted (or for fun, as animal rights terrorists would have you believe). This special issue has several papers on the growth of vivisections during the early times of this period, the 16^th and 17^th century.

• Gene similarity networks provide tools for understanding eukaryote origins and evolution. [OA]

There are two interesting and important aspects to this paper. The first is the insights into the endosymbiosis that led to the eukaryotes. The second is the one I am more interested in, and that’s the power of phylogenetic networks over phylogenetic trees. We have many phylogenetic trees of eukaryotes, but it was only with this paper and their employment of a network that we could clearly see the presence of the endosymbiosis, since a tree can only show one set of relationships – detecting things like endosymbioses and organismal fusions is simply beyond the scope of a phylogenetic tree, since a tree portrays hierarchical relationships where genes are passed vertically from parent to offspring, whereas an endosymbiosis is a relationship where genes are passed horizontally between unrelated organisms. Networks have no problem with such things, and can portray hybridisations, endosymbioses, reticulations, and other such phenomena that don’t fit into the standard basal-to-derived branching scheme of a phylogenetic tree. This paper is an example of this.

• A global assessment of the effects of climate policy on the impacts of climate change.

It’s well-accepted that science needs to play a dominant role when deciding how to deal with issues such as climate, not only because meteorology is a scientific discipline, but also because the scientific method has built-in mechanisms to check up on the effect of such policies and modify them as needed. Case in point: this paper, which examines how current climate policies are faring in the overall picture, if they are really working towards keeping the damage to a minimum or whether they’re just useless. We will not see the results of our work until at least the 2030s, according to the paper, and the conclusion is a rather obvious “the sooner the policies get to work, the better”, since a constant result is that the sooner emissions peak, the fewer the damages will be in the long run.

• From incipient to substantial: evolution of placentotrophy in a phylum of aquatic colonial invertebrates. [OA]

I recently wrote a tiny bit on bryozoan placentas, so here’s a paper with much more information.

• The G4 Genome. [OA]

G-quadruplexex are structure formed at the end of telomeres. Telomeres are repetitive DNA sequences at the end of chromosomes that get eaten away through the cell’s lifespan, acting as decoys so that the useful chromosomal DNA doesn’t get damaged. When you have four of them next to each other, they will fold with each other and form the G-quadruplex (G4). The G4 acts to stabilise the telomeres, and so have been actively researched over the past few years because telomere degradation is heavily implicated in cancer and ageing. It was also recently found that G4 complexes are found in other regions of the DNA molecule, not just at the bookends of it. If any of this stuff sounds interesting, this paper has a great summary of it all, and it also delves into a pretty cool discussion of how the genome ought to be viewed as a complex landscape rather than just a string of ATGCs. This biochemical stuff isn’t my cup of tea, but it’s interesting stuff anyway.

Papers of the Past 20 Days: 02.04 – 21.04.2013

It’s been a while, but I’ve kept them all the papers stored in a tab, nothing is lost. [OA] indcates open access papers. Feel free to request a detailed look at any of these.

General Interest, Important:

• Do men’s faces really signal heritable immunocompetence? [OA]

It’s no secret that I hold a low opinion of a lot of the human sexual selection and evolutionary psychology research, because I see a trend of insufficient sampling leading to overgeneralised statements that resemble “just-so stories” rather than evidence-backed claims. Here’s one paper that shows how to critically examine such papers.

Check out the whole range of additions, replies, and commentaries here, all [OA].

Tangentially-related, this review paper: Animal personality: what are behavioural ecologists measuring?

• Improved use of a public good selects for the evolution of undifferentiated multicellularity. [OA]

I always like to feature experimental evolution, especially when the results are as cool as this. Evolving multicellularity artificially isn’t anything new (e.g.), but more successful repetitions lead to us being able to identify all the potential evolutionary pressures that could have led to the convergent evolution of multicellularity, so such studies should always be encouraged.

Of course, studying things phylogenetically is also a good way: Development of ichthyosporeans sheds light on the origin of metazoan multicellularity [OA].

• Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution.

A point I made in my oft-read post on animal intelligence is that relative brain size is a fairly irrelevant criterion for intelligence. What matters more is organisation and connections between brain areas. While I was basing it on insects, the generality does also apply to mammals and vertebrates, as this paper shows: mosaic evolution is what leads to specialisations in the brain, and it’s what leads to the varying cognitive abilities of animals. Mosaic evolution in this case means a faster rate of evolution in some brain areas, which would automatically lead to novel connections. Relative brain size itself is irrelevant.

Some more on brains: Deep Homology of Arthropod Central Complex and Vertebrate Basal Ganglia.

• The genomes of four tapeworm species reveal adaptations to parasitism. [OA]

I’ve written before on what I think of most genome sequencing projects: largely meh. This is a case of a non-meh genome sequencing project, since it showcases the depths of adaptation in obligate parasites. As an invertberate zoologist, I’m intimately familiar with their various morphological contrivances, but what this genome project shows is that they are accompanied by fancy genomic specialisations too. That’s my main interest, although less hedonistic scientists would be interested in the medical advances enabled by these discoveries.

Of course, the genome that everyone was concentrated on this week was the coelacanth. I have no idea why, it must be that idiotic “living fossil” myth. Whatever. Here’s a link to it: The African coelacanth genome provides insights into tetrapod evolution [OA].

• Origin and diversification of the California flora: re-examining classic hypotheses with molecular phylogenies.

It’s of narrow interest, but thought I’d highlight it as shameless self-promotion: this is the sort of thing I wanted to do with arthropods when I came to Cyprus, but failed as a result of never receiving any funding.

• Molecular hyperdiversity and evolution in very large populations.

One of the points I tend to stick on when teaching evolutionary theory is the effect of population size. Very generally, the role of genetic drift (random evolution) gets larger as populations get smaller. Very large populations have their own wacky processes going, which this paper reviews and tells us to study deeper. I agree.

• Ecological traits and environmental affinity explain Red Sea fish introduction into the Mediterranean.

The Lessepsian migration is one of the more fascinating large-scale ecological phenomena happening nowadays. Since the Suez Canal was opened, the fauna of the Red Sea has been migrating naturally into the Mediterranean and, surprisingly, they’ve been outcompeting and displacing the native Mediterraneans. You can read some proposed reasons why in this paper. On a general note, I use this example to show that the distinction of “native” and “indigenous” ecosystems, while very useful for conservation, is not an evolutionary one. It’s a historical one, but just because species have evolved in the same place for centuries and millenia, it doesn’t mean they are a “perfect fit” – and this isn’t something we should expect anyway.

• Recovery of an Isolated Coral Reef System Following Severe Disturbance.

A slight ray of hope? Eh, depends on your perspective. Coral reefs may be among the most fragile of ecosystems, but this status is, in my opinion, very reflective of the disproportionate amount of attention that coral reefs get both from studies and from human anthropogenic disturbance – coral reefs get visited a lot, just look at any tropical tourism leaflet. This is what this paper shows, again in my opinion: leave coral reefs alone and they will rebound. Of course, ocean acidification is another problem altogether, but solving that is slightly more complex than slapping tourists and naughty fishermen around.

More coral research from this time period: Calcification by Reef-Building Sclerobionts [OA].

• Global Diversity of the Placozoa. [OA]

One of the biggest perks of being an invertebrate biologist is that you have the opportunity to learn and observe an enormous diversity of animal life. It’s much nicer than just being restricted to stupid mammals and birds and lizards and fish. It’s also great if you’re an educator, because kids tend to be informed only of charismatic animals: pandas, rabbits, cats. But this is a way too blinkered and narrow view of biodiversity, so introducing kids to the whole gamut of animal life is very satisfying. Here’s a review for the placozoans, the simplest animals yet known with only 5 cell types, with only one species officially described, Trichoplax adhaerens. It’s a marine 2mm large disc-shaped blob that constantly changes shape, and is more or less invisible in the wild – you need a stereoscope to see them properly. Go to www.trichoplax.com for pictures!

For another bunch of weirdo invertebrates: Molecular phylogeny of kinorhynchs; A complete three-dimensional reconstruction of the myoanatomy of Loricifera: comparative morphology of an adult and a Higgins larva stage [OA].

Another paper from this “Global Diversity” series from this time period, but involving stupid vertebrates: Global Taxonomic Diversity of Living Reptiles [OA].

• Deep-time patterns of tissue consumption by terrestrial arthropod herbivores.

I’ve already written about this very cool field of research, the study of plant-arthropod interactions through time and the useful info we get out of it. Here’s a review from the Grand Master of the field.

• Evolution and function of de novo originated genes.

New genes can arise fortuitously, but their gaining a fitness-affecting function is a more advanced prospect, and their fixation a rare event indeed, since the new genes must be integrated into the whole of the organism where domino effects, pleiotrop, and general chaos rule. This paper sketches a pathway for all those.

• Mechanical basis of morphogenesis and convergent evolution of spiny seashells.

One of my favourite aspects of developmental biology is the mechanical, physical basis for it: the effects of cells bumping into each other, the effect of cells moving through fluids, even the effect of gravity. Genes and developmental pathways are cool and all, but I have a special affinity for such holistic, big-picture perspectives that take external complicating factors into account. This paper provides an example of how important such things can be.

• The history and enduring contributions of planarians to the study of animal regeneration.

I think Easter is happening around now, not sure though. But I do remember writing a popular post on regeneration one year for Easter. Planarians feature heavily in it, and this review is useful if you want more details on why planarians are useful for the study of regeneration, and a historical perspective.

• Beetle horns and horned beetles: emerging models in developmental evolution and ecology.

Horned beetles are a classic model system for evolutionary ecology and evo-devo (and later will be for eco-evo-devo, or whatever the abbreviation will be). The interest arises because beetle horns are completely novel structures that arose convergently 6 times in beetles and were meaintained. Development informs us of how a novels tructure can arise in the first place; ecology tells us what they’re used for; evolution tells us how they remain. Put all that together, and you have a fascinating model system you can with hundreds of studiable species and permutations. This paper reviews all this potential.

If the meshing of evolution and ecology interests you, then so will this: Special Issue: A Critical Look at Reciprocity in Ecology and Evolution.

• Recent temperature extremes at high northern latitudes unprecedented in the past 600 years.

Crazy people with an agenda call us who follow the science on global warming “alarmists”. Here’s a paper to shove in their faces. Although the assumption that they know how to read is unwarranted and not backed up by the evidence.

• Embryology of Early Jurassic dinosaur from China with evidence of preserved organic remains.

China is the gift that keeps on giving in palaeontology. Some more amazing fossils.

But hey, other countries with cool fossils still exist: A ten-legged sea spider (Arthropoda: Pycnogonida) from the Lower Devonian Hunsrück Slate (Germany); A troodontid dinosaur from the latest Cretaceous of India; Original spotted patterns on Middle Devonian phacopid trilobites from western and central New York; A Large Accumulation of Avian Eggs from the Late Cretaceous of Patagonia (Argentina) Reveals a Novel Nesting Strategy in Mesozoic Birds [OA].

• Is Permanent Parasitism Reversible?—Critical Evidence from Early Evolution of House Dust Mites.

There’s been much fuss made about this in the popular science news. I took care of it on request some time ago on the Facebook page of the blog, so I’ll just copy-paste the text from there. It’s a solid phylogenetic study of mites whose main result is that dust mites are belong to a group of mites parasitic on vertebrates. In other words, house mites evolved from a parasitic ancestor. This is deemed surprising because parasites are rightly considered to be highly-specialised, so while a transition from generalist to specialist is easy to envision, the opposite is more implausible. But implausible is not impossible, as this study shows. The way the article is reported on belies the true nature of the advance here, especially witht he invocation of Dollo’s Law (which, to be fair, was done by the original authors as well). Dollo’s Law, as understood today (which is a far cry from Dollo’s original formulation), refers to a proposition that single complex characters, once lost, cannot be regained. But its validity as a law is increasingly being called into question, as more and more evidence piles on against its validity (see this paper, for example, which shows that fingers revolved in several liazrds even after they were evolutionarily lost). Saying that this paper puts “a new piece in the evolution puzzle” is just plain wrong. That piece has been known for ages. And in any case, a violation of Dollo’s Law is emphatically not “reversible evolution”, because that implies that evolution has a direction. The discovery is that the linear evolution to the free-living dust mite went like this: Free-living mites -> parasitic mites -> free-living dust mites. Does this mean that, somehow, dust mites have suddenly gone back in evolution? Absolutely not, because that would imply that they are now identical to those free-living ancestors of the parasitic mites. They’re not. They’ve gone their own way in evolution. So, to summarise: the awesome finding here, beside the details about mite evolution, is that free-living organisms can evolve from specialised parasitics. It’s not a reversal in evolution, except in the sense that their ecology is now similar to that of their distant ancestors. There is no such thing as “devolution”.

• Special Issue: Australopithecus sediba.

Those with a memory good enough for two years will remember the huge splash from two years ago from the description of Australopithecus sediba. For the uninitiated, enjoy a description I had written that time: They found pieces from two individuals: a 12-13 year old male, and an adult male. The age of the find is 1-98 – 1.75 million years, a time when there were many other hominins running around. The one closest to A. sediba, morphologically, is A. africanus: the body is very similar, with both being bipedal, but still having long arms (adaptation to trees). The face is also pretty much identical, besides A. sediba having slightly smaller teeth and more flattened cheeks. This is excellent, because A. africanus disappears from the fossil record before 2 Ma, so A. sediba fills in perfectly as their descendant, and so we get some more resolution of the australopithecine tree. A. sediba‘s hips have some feature found in Homo erectus, but not found in H. habilis and H. rudolfensis. The authors interpreted that as meaning that A. sediba is either ancestral to Homo (or very close to the ancestor), and that H. habilis and rudolfensis are not Homos, but actually australopithecines. Maybe I missed it when skimming through the paper, but I didn’t see them discuss the possibility that it’s convergence. After all, the hips are both adapted to bipedalism. It’s not far-fetched to think that they will look similar, and come up with the same mechanisms, to enable that. They then go into various arguments about Homo habilis not being a human ancestor, bringing in punctuated equilibrium to the mix. The whole issue has to do with how early Homos and australopithecines fit together – something that will always be controversial.

In any case, another big splash has been made, with another special issue devoted to A. sediba, with more papers with more detailed analyses and claims. Take your time poring through them, this is pretty critical stuff!

• The new micro-kingdoms of eukaryotes. [OA]

The phylogenetics and classifications of unicellular eukaryotes is something that invertebrate biologists are supposed to be familiar with, but I never had the interest in the microthings and don’t keep as close an eye on the advances as I should. Good thing reviews exist.

• Earliest evidence for the use of pottery.

Something for the archaeologists.

• The Ries impact, a double-layer rampart crater on Earth.

Only putting this here because it has personal significance for me: the Nördlinger Ries is the very first impact crater I went to as a student. Long-time readers should also be familiar with it: it’s the big brother of the Steinheim crater, where the lake that contained the Steinheim snails was. In fact, that post is a simplification of the field trip report I had to write when we visited the Nördlinger Ries. Ah, to be 6 years younger again. Good old days. Hmm.

Papers of the Week: 25.03 – 01.04.2013

Another week, another batch of new papers. [OA] indicates open access. Feel free to request a detailed look at any of these.

Important, General Interest:

• The origin of terrestrial isopods (Crustacea: Isopoda: Oniscidea).

Near the end of my post on tracheae, I mentioned that it would be interesting to use terrestrial isopods as models for investigating the convergent evolution of tracheal systems in all terrestrial arthropods. This paper echoes my thoughts exactly, and goes on to review what we know of their evolutionary history from their fossil record, relationships, and biogeography.

• Eulogy for Dieter Meischner (21 November 1934 – 24 May 2012).

One of the more influential geologists of the 20^th century, Dieter Meischner died last year. This great eulogy gives a glimpse of what he was like as a person and researcher.

• Deep metazoan phylogeny: When different genes tell different stories.

Those who know me would know that such a paper title hits all of my muttons:deep animal phylogeny has always been one of my major research interests, and the uncritical acceptance of molecular phylogenetics is one of my major pet peeves. Luckily, I’m not the only one with such tastes. This paper is one of several by Gert Wörheide examining the various inconsistencies present in current deep metazoan molecular phylogenetics, and how to fix them. I heard a lecture by him where he explained all of this, and his work is pretty exciting. This paper is an excellent showcase of how critical it is to properly sample your genes: every gene has a different history, and all those genetic stories do not match up to the species history – which is what we want to elucidate.

• New insights into the biodiversity and applications of cyanobacteria (blue-green algae)—Prospects and challenges.

Some cyanobacteria are already commonly grown for biotechnological purposes. Spirulina platensis is used to produce phycocyanins used in health foods and cosmetics, while Lingbya majuscule is used to produce immune modulators for pharmaceuticals. Nostoc commune and Aphanizomenon flos-aquae are also important species. The review goes through the classification of Cyanobacteria – a bit of a muddled mess – and explains their potential for all sorts of biotechnological and environmental applications.

• Complex cocktails: the evolutionary novelty of venoms.

If you’ve ever wondered about how widespread venoms are in the animal kingdom, how this hunting style evolves, and how we use this knowledge for medicine, then you want to read this review.

• Pitfalls, traps, and webs in ichnology: Traces and trace fossils of an understudied behavioral strategy.

If you’ve ever wondered how advanced the science of analysing trace fossils (ichnology) is, go through this paper.

• European origin of placodont marine reptiles and the evolution of crushing dentition in Placodontia.

Placodonts were one of the groups of marine reptiles that radiated in the Triassic, before disappearing at the end of the Triassic. They were most notable for having convergently achieved a turtle-like body plan with a bony covering on their underside. Their teeth were large, flat, and heavily-enameled, hinting at an animal that fed by crushing shells (molluscs, brachiopods). The excellent new fossil described in this paper is of a stem placodont, and shows the transition between the ancestral dentition and the specialised placodont shell-crushing teeth.

• Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. [OA]

I don’t usually care much for these genome-sequencing projects because they don’t tend to target species I consider important – basal ones that hold important clues to decoding phylogenetic history (the giant panda genome may be cool, but it’s useless to all but people who study pandas). This is an example of a good species to sequence: a lamprey, a basal vertebrate, a vestige of the era before vertebrate jaws evolved. Sequencing its genome holds a lot of promise in the quest to flesh out the events that led to the vertebrate radiation that we can’t tell from the fossil record and developmental biology. This paper already dishes out some answers, underlining the importance of innovations in the nervous system.

• Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.

I can’t say much about the actual results and their implications, I’m just putting this here so you can see just how advanced aDNA research and the associated technology has come. I was very (pleasantly) surprised when I read the title.

• Tubicolous enteropneusts from the Cambrian period.

Some (me included) say that Chengjiang and other Chinese localities have eclipsed the Burgess Shale by now, but the old quarry still has treasures to yield, as this paper proves. You can find numerous mentions of an undescribed Burgess Shale enteropneust in Simon Conway Morris’s papers (e.g. 1, 2), and I presume this is its long-overdue description.

Another awesome bit of exceptional preservation, also from this week’s Nature, this time from the Chinese Jehol biota: Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour.

• First steps in experimental cancer evolution. [OA]

Evolutionary medicine, using evolutionary theory to understand the mechanisms behind diseases, is a pretty exciting field, especially in its potential applications to studying cancers (see here, [OA]). This paper argues for investigating cancers with the tools of experimental evolution – putting cancer cells through the rigours of artificial selection to determine how they evolve, adapt, and their ecological limitations, which would then give us insights into how we can curb their proliferation in the body. I support this kind of framework.

Papers of the Past 10 Days: 14.03 – 24.03.2013

Papers from the past week. [OA] indicates open access. Feel free to request a detailed look at any of these.

General Interest, Important:

• Patterns of population epigenomic diversity. [OA]

It’s fairly common these days to hear epigenetics being trumpeted as the harbringer of a revolution in evolution. These calls are still immature due to a lack of studies showing that epigenetic changes are heritable. As far as I’m concerned, the ability of the genome to be epigenetically modified is very important for evolution since that ability is heritable and built into the genome, but whether the nature of the changes is fundamentally critical is still unclear to me, precisely because they don’t get passed on. This paper is an important step forward to figuring out the role of epigenetics in evolution: by analysing the epigenomes of an entire population of wild Arabidopsis, the researchers find that some genes always get epigenetically modified, and that this modification is important for proper plant development. In terms of the framework I outlined above, this means that the nature of some epigenetic modifications is so important that the ability to undergo that modification gets selected for, no matter whether the precise modification gets passed on or not.

See Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster, also from this week, for an example of the ubiquity of “traditional” microevolution.

• Breaking Haller’s Rule: Brain-Body Size Isometry in a Minute Parasitic Wasp.

Studying extremes in biology – the largest, the smallest, the most isolated, the most tolerant, etc. – always yields interesting observations. The smallest insects are various parasitoid wasps that are measured at sub-mm scales, and they are the focus of many morphological studies to see what happens at such extreme levels of miniaturisation. In terms of the nervous system, previous results have yielded such factoids as nucleus-less nerves, because a cell nucleus takes up too much space. This study shows that miniaturisation can also break one of the most constant rules of the animal kingdom: that relative brain volume increases with body size, i.e. that there is an allometric relationship between brain and body size. In Trichogramma evanescens, the parasitoid studied here, the relationship is isometric instead: relative brain volume is equal to body size, not larger. Whether this is generalisable, I can’t tell, but it would be interesting if so.

• Why coelacanths are not ‘living fossils’.

I find few things sillier than the notion of “living fossils”, because not only does it reveal misconceptions about the nature of phylogenies and evolution, in many cases, the “living fossils” are not even so closely-related to the fossils. This paper provides one such example, using the classical example of the coelacanth and showing that it’s not really close to the fossil ones. The sooner we get rid of this term, the better for everyone – those of us who try to educate the public suffer too much from having to deal with it, and it’s detrimental to public understanding of evolution.

Speaking of coelacanths, here are some new fossils from this week: Coelacanths from the Middle Triassic Luoping Biota, Yunnan, South China, with the Earliest Evidence of Ovoviviparity. [OA]

Remarkable Stasis in a Phloeocharine Rove Beetle from the Late Cretaceous of New Jersey (Coleoptera, Staphylinidae), also from this week, shows how to properly treat “living fossils”: they exhibit morphological stasis over an extended period of time. While interesting in and of itself, it doesn’t mean that Phleocharis is a “living fossil”. It just means that its particular trait of characters is successful enough, or that it has not encountered drastically new environments to cause major morphological changes, or it may merely be convergence. Whatever it is, the fossil Phleocharis described here is a distinct species that went on its own way in evolution, and the extant Phleocharis are not living representatives of it.

• Multicellularity arose several times in the evolution of eukaryotes.

This is a response to another paper, but serves as a great summary of how multicellularity evolved.

• Bat Predation by Spiders. [OA]

Just some good party trivia: spiders can eat bats. I wish it was published a teeny bit earlier so I could have included it in my spider lecture.

• Do American Crows Pay Attention to Human Gaze and Facial Expressions?

Cool new experimental behaviour paper reinforcing a well-known fact among ornithologists (especially those who’ve attempted to go through a bioethics committee), showing that wild crows react to human gaze, although they don’t distinguish between human expressions. Ornithologists conducting observations on wild bird behaviour are well aware of the delicate behaviour of birds and how sensitive they are to being observed, so this is a good paper to add to that literature.

• Darwin’s dilemma: The Steinheim snails’ point of view.

I’ve already written about the Steinheim Snails over here – their study by Hilgendorf resulted in the very first phylogenetic tree based only on fossil evidence. This paper provides a historical summary of how the tree then fared in the clutches of the anti-Darwinism movement of the early 20^th century (see end of this post), and its current state as a prime example of evolution and cladogenesis as outlined in my posts.

• Current Bibliography of the History of Science and Its Cultural Influences, 2012. [OA]

A 300-page bibliography for the history of science, for free. ‘Nuff said.

• The Oldest Brachiopods from the Lower Cambrian of South Australia. [OA]

Oldest anything deserves special mention, so here are the oldest brachiopods. Aksepasma saproconcha‘s the name.

• Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity. [OA]

My common quip these days is that the easiest way to find new species has stopped being running around the Amazon with a net, but to scoop up water from any source and sequence all the genetic material in there – something that’s now becoming increasingly cheaper with next-gen sequencing tech. This paper shows how this works and what kinds of results one can get.

Papers of the Past 10 Days: 04.03 – 13.03.2013

Papers from the past week. [OA] indicates open access. Feel free to request a detailed look at any of these.

General Interest, Important:

• Bigger is better: honeybee colonies as distributed information-gathering systems.

Since the beginnings of biology as a discipline, much has been written about eusocial insects and the successes they’ve achieved by cooperation. This paper highlights how cooperation has helped honeybees. Basically, it finds that larger colonies find out more information about their surroundings because they have more flexibility to adjust the size of their foraging parties. After each scouting trip, the bees come back and make a report, and the optimal group size of foragers is chosen to get distributed to the scouted areas. There is no competition between the foragers in this system, it’s all cooperation for the ultimate good of the colony.

• Phylogenetic analyses of termite post-embryonic sequences illuminate caste and developmental pathway evolution.

While the development of castes in eusocial insects is mostly determined by the environment and related epigenetic modifications, the capacity for such developmental diversity is a genetic feature. This paper stresses the importance of that last bit by finding that during termite evolution, that capacity evolved independently multiple times. In other words, it’s not an automatic feature that can be invoked at will, but one that had to evolve and be selected for.

This related paper was also published this week: Evidence of a conserved functional role for DNA methylation in termites.

• Special Issue: Philosophy and the Microbe.

Philosophy is not everyone’s cup of tea, so that’s not the reason why I’m putting this special issue as important and of general interest. I’m highlighting it because the papers in the issue all center around bacteria and viruses and other unicellular that are, quite frankly, given short shrift in the majority of biological discussions – we often need a microbiologist to come and remind us that they exist and are actually more important than the enormous multicellulars. I occasionally make the mistake too, but am trying to change both myself and everyone else. So read this special issue and get your hands on Jan Sapp’s The New Foundations of Evolution. You won’t regret it.

• Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution.

As a distinct critic of molecular clocks, I urge much caution when reading this paper. However, I will say that the underlying phylogeny is satisfactory, as is the number of fossil calibrations, so the results are more reliable than any previous molecular clock study going back to the Cambrian (which, really, isn’t saying much considering the horribleness of some of those previous results). Molecular clocks will always overshoot the actual divergence time – it’s an inevitable feature – and the amount of overshooting is compounded the further back in time you go. This can only be tempered by copious fossil calibrations. My own opinion on the conclusions here is that I accept all of them except Ediacaran origin of ecdysozoans (fossils are the only thing that will sway me). I also find the presented radiation time for onychophorans and tardigrades meaningless, because it’s only for extant ones, whereas onychophorans and tardigrades have a much deeper pedigree to uncover.

• Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae).

Who doesn’t like studies on evolution in caves? Everyone knows about eyes being reduced and eventually lsot in caves. Despite this though, rhodopsin and other visual pigments tend to stay functional in cave-adapted organisms, most likely because they have other roles (e.g. in circadian rhythms). This paper shows that even then, the pigments can eventually get corrupted: several lineages of amblyopsid fish that have been in caves for over 10 million years have independently accumulated enough rhodopsin mutations that it’s now non-functional.

• The anus as a second mouth: anal suspension feeding by an oral deposit-feeding sea cucumber.

Excellent party trivia: some sea cucumbers use their anus as a second mouth. I’m sure there’s an insult to be constructed out of this.

More great party trivia: Biomechanics and hydrodynamics of prey capture in the Chinese giant salamander reveal a high-performance jaw-powered suction feeding mechanism. [OA]

• Dynamics of a Snowball Earth ocean.

Regardless of just how ice-covered the Earth was, whether there was a true “Snowball” Earth or whether it was just a “Slushball” Earth, there’s a general agreement that the ocean underneath was fairly homogeneous and inactive. Not so, as this modelling paper shows: even with a 1km crust of ice, there would have been circulation around the Equator, coastal upwellings of warmer waters, and eddies all around.

• Deconstructing morphology: reply to Scholtz (2010).

I don’t usually like linking to such forum articles where opinion reigns, but I consider this exchange important in light of the trend of modern biology to marginalise traditional morphological analyses. Make sure to read the original article by Scholtz first, then this reply, then Scholtz’s reply from this same issue. They can be rather esoteric, dealing with criteria for homology and the importance of cladistics, but if you’re interested in the role of morphology in modern evolutionary biology or are curious about it, you may find some interesting nuggets.

• Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote.

Very cool discovery – up to 5% of Galderia sulphuraria‘s active genes were received by HGT from bacteria, and they allowed the alga to live in its hot, sulphidic and acidic environment where not much else can survive.

• In the aftermath of the end-Permian extinction: the microbialite refuge?

Speaking of extreme environments, the ocean after the Permian-Triassic extinction was probably not a nice place to be in… unless you’re a herbivorous micro-animal like an ostracod, in which case you can seek refuge in and feed on the microbialites that spread wide after the aftermath, as this study of Early Triassic ostracods shows. For those not in the know, microbialites are structures formed by microbes precipitating minerals around them. Biofilms and stromatolites are the most famous types of microbialites.

• New insights into differences in brain organization between Neanderthals and anatomically modern humans.

Modern humans went towards high sociality and cooperation at the expense of physical growth, while Neanderthals built on their Homo heidelbergensis heritage and added more body mass and became more physically robust. The authors could tell all this just by measuring brain endocasts and eye socket sizes. I may not like vertebrate palaeontology, but the amount of reliable extrapolation they do is amazing.

Papers of the Week: 25.02 – 03.03.2013

Papers from the past week. [OA] indicates open access. Feel free to request a detailed look at any of these.

General Interest, Important (unsorted):

• Special Issue: Fostering Advances in Interdisciplinary Climate Science.

The papers of this special issue showcase how multifaceted the modern study of climate change is, incorporating atmospheric science to geology to ecology to social sciences, and more. I consider this important to realise and take notice of, as it stresses just how much of a concerted effort is needed to achieve the results that the IPCC presents in its Assessment Reports, for example – and also underlines the unlikelihood that the entire field is a scam, which is an idea brought forth by dangerously delusional quacks.

• Detection and attribution of anthropogenic climate change impacts.

Continuing with the theme of climate change, this review paper summarises how we really can pinpoint the causes of current climate changes to human influence. If you have doubts about anthropogenic global warming, then this is the paper for you.

• Xenoturbella bocki exhibits direct development with similarities to Acoelomorpha. [OA]

I’ve outlined Xenoturbella in this post, including the important kerfuffle over its phylogenetic placement. This study finds that the development of Xenoturbella is very similar to that of an acoel, providing further support – and, significantly, from a source other than molecular phylogenetics – for the Xenacoelomorpha taxon. However, the position of the Xenacoelomorpha within the general tree of animals is still up in the air – is it a basal bilaterian taxon, or is it nested somewhere within the Deuterostomia as phylogenomic results suggest?

• A Precambrian microcontinent in the Indian Ocean.

I place this paper here because it shows how quickly our knowledge in geology can change. I notice a lot of general ignorance about how geological advances are made. Many people don’t realise that geological maps are still drawn by hand during fieldwork, and that that’s how significant findings are made, for example. Anyway, this is far more sophisticated – geophysics and geochemistry hinting that Mauritius lie on an ancient, Precambrian microcontinent that split off from Madagascar in the early Tertiary.

• Embryos, polyps and medusae of the Early Cambrian scyphozoan Olivooides.

Olivooides has long been known as one of the more spectacular examples of fossil preservation, showing a nearly-complete developmental sequence from embryonal stages (Bengtson & Zhao, 1997). The specimens have always pointed to a scyphozoan affinity, and this paper reinforces that by examining even more awesomely-preserved specimens where the internal anatomy is visible.

• Disposable penis and its replenishment in a simultaneous hermaphrodite.

Placing here only because of the juvenile comedy value of “disposable penis”. And yes, it’s exactly what it sounds like: a sea slug that throws away its penis after mating, then grows another one again. My zoologist subconscious does have an idea for future research: is this mechanism somehow related to the evolution of the “love darts” of gastropods? It’s most likely a crazy idea, but who knows.

• Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs.

Besides having a great methodology, I find this paper a neat demonstration of natural selection in action and will be incorporating it into my relevant lectures.

• Jaws for a spiral-tooth whorl: CT images reveal novel adaptation and phylogeny in fossil Helicoprion.

Edestid sharks were, back in the Permian, the dominant predators. Nowadays, they serve as a laughing stock for first year palaeontology students, who tend to find the coiled teeth that they sported menacing but ultimately ridiculous. This paper advances our knowledge of Helicoprion, the most famous of these weirdos, including details on how the tooth whorl fit into the jaw. Very interesting stuff; if you need an example of a cool and exotic-looking fossil, I recommend this paper.

• Specialized appendages in fuxianhuiids and the head organization of early euarthropods.

The only taboo subject on this blog is the evolution of the arthropod head, so I will not comment on this unless requested. Suffice it to say that it’s an important paper, although it won’t go down lightly.

• Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus. [OA]

Batrachochytrium dendrobatidis is a fungal pathogen of amphibians, causing the lethal disease chitridiomycosis. The pathogen and disease are so harmful that they’re single-handedly responsible for the decline in amphibian populations and species worldwide – the spread of the disease is currently being thought of as the primary factor causing the currently ongoing global amphibian extinction. Hence, studying it is of utmost conservation importance, and this paper is an important step forward, amassing geographical and epidemiological data in order to map out the global extent of the disease and its taxonomic reach, identifying which regions and taxa are most at risk.

• Enigmatic Liaisons in Lepidoptera: A Review of Same-Sex Courtship and Copulation in Butterflies and Moths. [OA]

I deal with deeply-ignorant homophobes all the time, especially when I see them claim that homosexuality is “unnatural” and “against evolution”. My usual response is a dump of papers showing rampant homosexuality in the animal kingdom. It puts things into perspective. Here’s a review of homosexuality in lepidopterans, a good addition to the anti-idiotic-homophobe literature.

Papers of the Week: 19.02 – 24.02.2013

Your papers for the week. [OA] indicates open access. Feel free to request an in-depth look at any of these.

Important, General Interest:

• Shedding light on light: benefits of anthropogenic illumination to a nocturnally foraging shorebird. [OA]

Human modifications to the environment fall on a spectrum from totally destructive (e.g. open-cast mining) to positive (e.g. land rehabilitation). Most activities have aspects of both: agriculture destroys the original landscape, but if managed properly can become a local biodiversity hotspot. Artificial lighting appears to be one of these dual-sided aspects. Light pollution is being increasingly recognised as a serious problem for many animals who navigate using moon- and starlight (see this paper). However, this paper shows that artificial lighting is a boon for foraging shorebirds, who much prefer using eyesight than pecking randomly. With the artificial lighting from an industrial complex at the research location, the studied shorebirds could forage more and exclusively by sight, so it’s an undeniable benefit for them.

• Dung Beetles Use the Milky Way for Orientation.

I’ve written about how ants use the night sky for navigation in this post. Dung beetles are another model organism for studying navigational systems, and this paper demonstrates why: they can use the galaxy for orientation – this was tested in a planetarium. A related paper with a self-explanatory title from this week: Evidence for Geomagnetic Imprinting as a Homing Mechanism in Pacific Salmon.

• Ant Pupae Employ Acoustics to Communicate Social Status in Their Colony’s Hierarchy.

This is pretty cool: pupae that can stridulate (make sounds). Not only that, the stridulation informs nestmates of what the pupa’s place in the social hierarchy is.

• Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. [OA]

A very interesting paper showing convergence at the genetic level in experimentally-evolved E. coli populations that converged on the same ecological phenotype (the ability to digest a different food source). In other words, despite going their own way evolutionarily, they acquired the exact same mutations as each other to form the same overall phenotype in reaction to a similar environment. You can glean an explanation for this from my natural selection post; search for “What Kramer et al.” and read the paragraphs. If you still can’t figure it out, ask. The other big story with this paper is the methodology that enabled this finding: the sequencing of so many isolates from the different populations at different periods. It’s quite a large undertaking, and it hints at the possibilities of an exciting future when we can investigate such microbial ecological changes at the genomic level with relative ease. Needless to say, that will be an awesome future.

• The Bilaterian Head Patterning Gene six3/6 Controls Aboral Domain Development in a Cnidarian.

A typical deep homology research paper, but with the interesting conclusion that the same genes control the development of the aboral region of cnidarians and the bilaterian head, therefore those two regions are homologous, obviously important for elucidating the evolution of the head, which is directly related to the evolution of a central nervous system. This isn’t a new hypothesis, but the evidence rpesented here is very compelling in its favour.

• Fruit Flies Medicate Offspring After Seeing Parasites.

Nothing groundbreaking here, just cool behaviour. Endoparasitoid wasps are nasty creatures, spending their larval stages on or in the parasitised host and feeding on it while it’s alive. Obviously, they should be avoided, and it seems that female Drosophila use their memory to do just that. This study shows that if the female, in her lifetime, sees a female parasitoid wasp, she will lay her eggs in a more alcoholic substrate that the wasp won’t come near. This behaviour is based purely on memory – it doesn’t matter if the wasp is present during egg-laying; if the fly has an image of the wasp, she will modify her oviposition behaviour.

• Impacts of ocean acidification on marine seafood.

I’ve written about ocean acidification over here. In a seashell (might as well use this bad wordplay while seashells still exist): the excess carbon dioxide we’re pumping relentlessly into the atmosphere is dissolving into the ocean, causing it to become more and more acidic. Hijinks ensue. Organisms that depend on calcium carbonate are most at risk, since the carbonate will be corroded by the acidic waters.In terms of human food impact, which is what this review focuses on, what this means is the coral reefs will be severely affected, which destroys the habitats of many fish. You can say goodbye to the shelled molluscs; calamari and squid will be the only cephalopods you will be eating. Shrimp and crabs will be unaffected, as far as can be predicted.

Papers of the Last Month (!): Jan 21 – Feb 18, 2013

So I got really busy and am forced to compile a month’s worth of papers into one post. Happy reading. By the way, I have made a Facebook page for the blog which you can like and follow and write on, and all the informational posts are also getting uploaded on Glipho.

[OA] indicates open access papers. For detailed discussion of any of these, feel free to request!

Must-Read Papers (unsorted):

• Special Issue: The polyandry revolution.

Polyandry is when a single female mates with multiple males, a mating system that isn’t uncommon among animals. Polyandry comes in many flavours, and bears significant costs (injury, energy expended during repeated mating, predation risk) that are recouped by the reaped benefits (selecting the father, more parental care, more genetic diversity for offspring). This special issue reviews all aspects of the evolution of polyandry in the light of the latest research in ecology and evolutionary theory. Two [OA] papers.

• The origins of multicellular organisms. [OA]

The very common misconception of evolution having a direction or preferred goal is most commonly manifested when people ask “why aren’t all animals intelligent?”, or “why are bacteria still unicellular?”. In the latter, the thought process is that multicellularity is a trend that all “higher-evolved” organisms undergo. This is, of course, completely wrong. Multicellularity is a rarity that only has three major occurrences – plants, fungi, animals. The rest of the diversity of life – which far outnumbers the diversity of these three clades – is unicellular. Thus, the real interest in multicellularity isn’t “Why aren’t these organisms multicellular?”, but “Why are those other organisms multicellular?”. Multicellularity is the weird exception, not the trend to be followed. This paper reviews the origins of multicellularity in all organisms that express it, and answers the mechanical and molecular genetic details of this question: it’s all cell adhesion, communication, and specialisation, tissue pattern formation, and morphogenesis. If you need a review of these things, then this paper is perfect.

• Artificial Selection on Relative Brain Size in the Guppy Reveals Costs and Benefits of Evolving a Larger Brain.

In the description above, the first question I mention is “Why aren’t all animals intelligent?”, with the questioner almost always defining intelligence as modern human-like intelligence. Not only is that a stupid definition, it also implicitly assumes that having a human brain is all nice and dandy. Not so. The human brain is a gigantic lump of inefficiency, the equivalent of a supercomputer built by a five year old with unlimited resources. The energy needed to grow and maintain our brain (and thus acquire and keep our intelligence) is truly immense, and this is a cost that we can bear only because of we’ve managed to get ourselves a fancy supply of constant food. This paper provides direct empirical evidence for this energy-cognition trade-off using experimental evolution on guppies: large-brained guppies end up smarter, but also produce less offspring and have smaller guts.

• Nutrient-Mediated Architectural Plasticity of a Predatory Trap. [OA]

Another popular misconception to take down: genetics are not a blueprint. I get a surprising amount of people asking me whether spiders decide hwo their webs should be and if they can customise them. Of course they can. Phylogeny predicts the general architecture of the spider web, whether it’ll be an orb or a sheet or dragline, but only because different spider taxa have different leg and spinneret arrangements and so are physically incapable of building different web types. But the fine details of the web – how dense the threads should be and even how sticky they are – are all determined by the spider depending on its situation. This paper provides a demonstration of that, where amount of food available causes significant changes in web architecture. This is not genetically-determined, it’s just a reaction to the ecological circumstances.

• Experimental Evolution of Adaptive Phenotypic Plasticity in a Parasite.

A great example of experimental evolution, the researchers created a virus that has a flexible life history by selecting for multiple infection. When acting alone, the virus kills its host slowly, when others are around, it kills its host quickly. That such flexibility is exhibited by disease-causing viruses in the wild makes this research important as well as cool.

• Experimental evolution of heterotrophy in a green alga.

Another great experimental evolution paper, this time growing photosynthetic algae for so long in the dark that they evolve to become incapable of photosynthesis.

• A Color-Mediated Mutualism between Two Arthropod Predators.

One of the most insightful things I learned in zoology was that there are no hard lines distinguishing symbioses, mutualisms, and parasitisms. All these interactions are on a spectrum from fully beneficial to both parties to fully detrimental to one party and fully beneficial to the other. This paper provides a case in point to the fluidity of species interactions: when two predators interact, it’s usually a kleptoparasitic interaction, with one predator stealing the other’s food. However, the researchers here show that the spider Cyrtophora unicolor allows the smaller spider Argyrodes fissifrons to get on its web and take small prey, because the shiny colour of A. fissifrons attracts moths for C. unicolor to feed on. Both predators have entered into this mutually-exploitative and mutually beneficial interaction; it may be that in the future, the interaction will shift to another side of the spectrum and one will become parasitic on the other (C. unicolor enslaving the smaller spider, or the smaller spider becoming a true kleptoparasite).

• Do people “personally experience” global warming, and if so how, and does it matter?

The first thing you experience as a science communicator is that most people want to be given an excuse to learn something. It must have some sort fo practical application in their lives, or it must be something they can see for themselves. While this is based on my personal experiences with public lectures, this paper confirms this in the case of global warming: if people feel like they’re “experiencing” global warming, they’re more likely to accept it’s happening. Of course, this also brings up the thorny issue of the misconceptions about global warming – the classic confusion of short-term weather patterns with long-term climate change, a blight on the popular conception of climate change.

• Reduced plumage and flight ability of a new Jurassic paravian theropod from China.

Yet another feathered dinosaur around the early origin of flight, although Eosinopteryx here couldn’t fly, it was more a runner; I imagine it like the flightless birds of today.

• The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid.

Today’s echinoderms (brittlestars, sea stars, sea lillies, sea urchins, sea cucumbers) are a tiny vestige of echinoderms’ past disparity. While these extant echinoderms are characterised by pentaradial symmetry, their early fossil record shows a wealth of different body plans, including bilaterally-symmetrical ones that had sown some confusion by being thought to be a link between chordates and echinoderms. This paper describes two Cambrian localities from Morocco with well-preserved echinoderms. When combined with the knowledge we have of other Cambrian echinoderms, we get the insight from the title: the very diverse echinoderm body plans (all but one of which are now extinct) emerged very quickly, in a timespan of 10-15 million years.

• Relationship between sea level and climate forcing by CO2 on geological timescales.

A favoured “weapon” of global warming opponents is their fallacious trotting out of geology to point out that Earth’s climate has always varied, so why raise the alarm over a couple of degrees of warming. This is a fallacy because we don’t care about the Earth, we care about ourselves and our future survival. The Earth isn’t affected by global warming, or anything else we do for that matter (unless we start messing around with the core, or install a giant rocket booster and push the Earth into the Sun). And what geology tells us is that climate forcing has always had drastic impacts on both geomorphology and the biotic sphere. This paper shows how CO₂ levels in the past 40 years have affected sea level, and predicts that even if we keep CO₂ levels as they are now, we have a 68% chance of getting a 9+m rise in sea level. That’s a lot of major cities and little islands drowned (and even some mainland countries too, like most of Bangladesh).

• Record-Breaking Early Flowering in the Eastern United States. [OA]

Record-breaking temperatures followed by record-breaking phenological changes. I’d tell you to expect more papers showing changes in insects, but there’s already a ton of them…

• Climate-driven changes in northeastern US butterfly communities.

… like this one.

• Larvae of the parasitoid wasp Ampulex compressa sanitize their host, the American cockroach, with a blend of antimicrobials.

Humans aren’t the only animals who clean their food.

• In vitro antimicrobial sperm protection by an ejaculate-like substance. [OA]

Bed bugs go even further and keep their sperm germ-free.

• Insights into bilaterian evolution from three spiralian genomes. [OA]

While this paper isn’t a must-read itself – it’s just a reporting of three new genomes – I consider this an important step, sicne these genomes can now be incorporated into a new phylogenomics analysis of the animals, which might prove fruitful. I do have one qualm though: the organisms they picked are model organisms, but like with most model organisms, they’re not really basal within their own clades, making their utility for phylogenetics that much more limited. Still, better than nothing, I suppose.

• Can We Name Earth’s Species Before They Go Extinct?

Must-read only in the sense that this makes an excellent journal club paper to be dissected, an activity I did with a colleague’s class via Skype. Read it to sharpen your skepticism and critiquing skills. (Technically, that’s how you should treat every single paper, but some are more amenable to such things…)

• The magnetite-based receptors in the beak of birds and their role in avian navigation. [OA]

The way birds can use the magnetic field for naviation is always fascinating, although I profess a casual ignorance of the details. All I knew prior to this paper is that they have magnetic pigments in one fo their eyes that allow them to “see” the magnetic field, but apparently it’s much more complex as this review shows. It concentrates on the beak and its innervation, showing that the magnetic receptors there record the strength of the magnetic field.

• Altruism across disciplines: one word, multiple meanings.

One of my biggest pet peeves is the conflation of evolutionary altruism (where helping and selfishness are defined purely from the consequences on allele frequencies) and social altruism, which is a behavioural, cultural, sociological thing that, in my opinion, has nothing to do with the altruism of evolutionary theory. This paper dissects the various uses of “altruism” in different disciplines, and gives them a neat descriptive adjective to help us all not talk at cross-purposes. I like it, although I know many who will scoff at these separations (they’re the same people who trigger my pet peeve).

• Iodine-129 concentration in seawater near Fukushima before and after the accident at the Fukushima Daiichi Nuclear Power Plant. [OA]

They’re elevated… but still nowhere near being significant for human health. The anti-nuclear crowd really has their work cut out for them.

• Recurrent Early Triassic ocean anoxia.

It’s rare for any extinction to be sudden – the majority of extinctions are culminations of increasing stresses, or they’re the combinations of many local pulses of extinction that geology compresses into one major event. The Permian-Triassic extinction is the latter, with detailed dissections of earliest Triassic localities from around the world showing wildly different patterns of recovery and extinction. This paper is also a demonstration of this, by showing that there was no gradual trend of recovery from the P-T. Instead, recovery took place in quick, local bursts that repeatedly got stamped out by local extinctions. When you zoom out, it appears as though the earliest Triassic was dead; but when you zoom in, it was a boom-and-bust cycle.

• The impact of global climate change on genetic diversity within populations and species.

A good review for those interested on the effect of climate change on the biosphere.

• The earliest rugose coral.

Oldest anything deserves a mention, so here’s the oldest finding of a rugose coral to date, from the Mid-Ordovician of Iran.

• Evolutionary Biology for the 21st Century. [OA]

While technically an opinion piece, not a research or review paper, I think this must be read by everyone, because it summarises why evolutionary biology is important and some of the upcoming research directions that we evolutionary biologists are getting into. It gets many kudos from me for including the importance of natural history collections (critical in a time when museums are facing unprecedented budget cuts) and for reminding everyone of the utility of the fossil record. Definitely a teaching piece as well. Read it now.

• Niches and neutrality: community ecology for entomologists. [OA]

Another good paper for teaching, consider this a “community ecology for dummies” primer. If you’ve always been interested in what community ecology is and what the main fights in it are, then read through this paper.

• Variation and constraint in Hox gene evolution.

Hox genes are wellknown as master genes, responsible for deciding where body parts go on the body (you can make flies with antennas for legs by changing Hox gene expression, for example). So they’re naturally considered very important for the evolution of body plans, so their evolution is always getting studied. This research looks at one particular Hox gene, fushi tarazu (ftz), which is not involved in patternign the body, but is instead involved in the formation of the central nervous system, only being expressed in neural cells. This unique function it got was a cooption from its ancestral role, whatever that was, showing that even these master genes are subject to the same forces as other genes.

• Slime through time: the fossil record of prokaryote evolution.

An overview of biofilms and microbial mats and their presence in palaeontology.

• Involvement of microbial mats in delayed decay: an experimental essay on fish preservation.

Speaking of microbial mats, their most useful role in palaeontology is as a cause for exceptional fossil preservation. A lot of soft tissue preservation in the fossil record is caused by the action of microbial mats conquering carcasses and depositing hardy minerals while digesting the tissues. Pyritisation is the most famous case. Even when they don’t directly cause soft tissue preservation, they may delay decay until appropriate conditions set in, or even form a coffin around the carcass where the appropriate conditions for soft tissue preservation prevail. The latter case is what is shown in this paper using Recent fish.

• Tapeworm Eggs in a 270 Million-Year-Old Shark Coprolite. [OA]

Speaking of exceptional fossil preservation, how about some fossil parasitism? Everyone should know tapeworms: they reside in vertebrate guts and release loads of eggs to be shat out. In this cae, the vertebrate victim was a shark, and its feces kept them entombed for 270 million years – the earliest cestode fossil to date.

• Nanometer-scale characterization of exceptionally preserved bacterial fossils in Paleocene phosphorites from Ouled Abdoun (Morocco).

Just some more mindblowing preservation.

• Agent of Whirling Disease Meets Orphan Worm: Phylogenomic Analyses Firmly Place Myxozoa in Cnidaria.

I wrote a post about the Myxozoa here, mentioning that there is absolutely no solid hypothesis for their phylogenetic placement within the animals. We now have a reasonably-evidenced hypothesis presented in this paper: myxozoans as cnidarians, close relatives to the Medusozoa. The tree is solid, but I really have doubts from a zoological perspective. Parasites are notorious for their ability to baffle morphologists like myself, but a loss of all cnidarian traits is a bit too much for me to swallow, so I’ll wait for someone to find some vestige of a cnida before hopping on board this train.

• Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud.

I find the atmospheric biome to be fascinating to imagine – loads of bacteria floating around in air currents, under extreme conditions (cold, radiation) and acting as nucleation centers for cloud formation. It’s pretty wacky. This paper looks at the biogeochemistry of hailstones and even manages to culture bacteria from them.

• The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals.

A great methodological paper, but I cannot for the life of me understand why this is published in Science, which provides no room for proper exploration of such data-rich papers. A proper monograph is hopefully in the works.

• Epigenetics for behavioral ecologists.

Epigenetics is commonly trotted out in popular science as the Great New Thing that will supersede evolution and explain everything that we can’t explain already, especially when it comes to behaviour. If you want to go past these bullshit overstatements, this paper is a good start.

• From natural to artificial photosynthesis.

One of the goals most looked forward to in synthetic biology is the replication of photosynthesis. I don’t really see why – photosynthesis is really not an efficient process, so I don’t see the point of trying to replicate it. But then again, I’m not a synthetic biologist, so what do I know. In any case, this paper outlines the state of the art.

• The peppered moth and industrial melanism: evolution of a natural selection case study.

The peppered moth is the classic example used for teaching natural selection – see my natural selection post as an example. This paper reviews all its aspects, right down to the genetics and the missing pieces of knowledge. Highly-recommended. See also this related paper from the same issue.

• The naked planet Earth: Most essential pre-requisite for the origin and evolution of life.

A summary of the geological background necessary for the evolution of life.

Papers of the Week: Jan 14-Jan 20 2013

After last week’s linkfest, readers wrote in saying a hybrid would be best: important papers with descriptions, and just links for papers that are of more esoteric interest.

101 papers this week, 15 open access (search for [OA]).

Must-Read Papers (unsorted):

• Significant changes in land vegetation and oceanic redox across the Cretaceous/Paleogene boundary.

This paper examines the impact of the K-T on terrestrial vegetation in a section in Spain, using biomarkers tot race the succession of events recorded in this particular locality. Summary: at the event, the vegetation was destroyed, and an increase of terrestrial material deposited in the anoxic oceans is recorded. Then, 10000 years later, conifers rebounded.

• Life as a Cataglyphologist—and Beyond.

Part scientific autobiography, part history of research, this is a review of Rüdiger Wehner’s work, written by himself. If you don’t know who he is, read my post on ant navigation and realise that the bulk of it is derived from his work using Cataglyphis ants as a model organism.

• Recurrent Evolution of Dependent Colony Foundation Across Eusocial Insects.

There are several ways in which eusocial insects start a new colony. There is solitary founding, in which a single queen moves to a new nest. Pleometrosis is when several queens move together. There is social parasitism, in which a queen attempts tot ake over a foreign colony. And, finally, dependent colony foundation, in which a queen and several nestmates move together to the new nest. Each strategy has its own distinct advantages, with the main ones of DCF being that the success rate is high, that the new colony can get to work immediately, and that the colony size can be optimised by choosing how many workers to take. These are strong benefits, and this is why it’s evolved convergently in many bees and ants. This paper reviews just how many times it’s evolved and the various quirks species have added to the strategy.

• Nutritional Ecology of Entomophagy in Humans and Other Primates.

Insects will inevitably be part of our diet in the future – it’s unavoidable, given that agriculture will soon be failing all around us. It’s nothing to worry about: only we weird Westerners avoid eating insects because we’re taught that they’re icky. In fact, insects have always been a staple of primate diets, including human diets. They’re very nutritious, and the only difference to chicken is that the exoskeletons are a bit crunchy. Read this review to get a broad perspective on entomophagy.

• Conservation and Variation in Hox Genes: How Insect Models Pioneered the Evo-Devo Field.

For anyone interested in an overview of evo-devo, this paper is a must-have. Besides the short historical and thematic overview, it provides many examples of fundamental evo-devo research in insects, and makes an excellent resource for any lecture on the topic.

• A History of Entomological Classification.

For anyone interested in the history of entomology, get this paper, which summarises how insect systematics has changed from antiquity to today.

• Ants and the Fossil Record.

A review of the fossil record of ants.

• The Early Evolutionary History and Adaptive Radiation of the Pterosauria.

It seems that pterosaurs hit on a winning evolutionary formula with their flying body plan. This paper analyses all the various phylogenetic hypotheses for early pterosaurs and finds that all of them share one thing in common: pterosaurs experienced an adaptive radiation very early on. This is most probably due to being the only large animals to fly at the time, similar to how birds are now highly-successful.

• Recurrent jellyfish blooms are a consequence of global oscillations. [OA]

It’s quite common to see articles, both popular and scientific, citing sudden blooms of jellyfish as warning signs of a dying ocean. Try as you might though, you will find little evidence backing such an assertion up, except for local reports of increased jellyfish numbers in warmer waters near industrial discharge sites. This paper looks at the occurrence of blooms and finds that there is very little statistical support for an increase in jellyfish over time (correlated with degradation). Rather, there is a global, 20 year cycle that jelly blooms go through.

• Hybridization and speciation. [OA]

A review and many comments, all open access, on the relationship between hybridization and speciation – an important topic, given that hybridization has a chance of occurring in the short- to mid-section of speciation.

• Repeated innovation in great apes.

This paper is a significant experimental demonstration of the intelligence of great apes. The authors tested the innovation of all non-human great ape species, their ability to come up with modify their past solutions to new problems, and found that all but the orang-utans aced the tests. This means they’re able to think about and learn to overcome new challenges – just like humans.

• Thelytokous Parthenogenesis in Eusocial Hymenoptera.

I wrote about parthenogenesis here. This paper reviews thelytoky in eusocial Hymenoptera, a strange form of reproduction in which female offspring come out of unfertilised diploid eggs (usually, unfertilised eggs result in males).

• Origins of the supercontinent cycle.

The supercontinent cycle is a proposed pattern of the Earth going through cycles when the continents are joined together. Its acknowledgement is fairly significant, and this paper reviews the history of research on the matter, from its first propositions and realisation of multiple supercontinents through time, to its modern acceptance and milestone publications, to future prospects.

• Mosquito ecology and control of malaria. [OA]

Mosquitoes aren’t just annoying critters and important prey in freshwater habitats. In developing countries, they’re a huge public health hazard as vectors of Plasmodium, the protozoan that causes malaria. Proposals to control them have ranged from insecticide flooding to biocontrol using parasites and prey to draining of wetlands to targeted biomolecular interventions – and none of these work by themselves. Thsi paper sets the conversation on the right track by stressing that before we can control them, we need to understand every bit of their ecology.

• Styles of scientific reasoning: Adolf Remane (1898–1976) and the German evolutionary synthesis.

Adolf Remane is one of the most important modern zoologists to have lived, his most famous contribution arguably being the setting of the three critical criteria for homology. However, history has not treated him well due to the influence of Ernst Mayr, who, for some reason, found his contributions to not be so useful. This was a mistake on Mayr’s part, as this paper shows: by analysing what Remane wrote of, and analysing what Benhard Rensch (another zoologist who Mayr consistently praised) wrote of, the paper finds that the two are not really so different. I hope this promotes Remane’s work again, because while it’s somewhat outdated now, and he got some things plain wrong (e.g. he viewed palaeontology as useless for phylogenetics), he was still a significant part of the 20^th century’s biology that gave birth to the Modern Synthesis.