Papers of the Week: Jan 14-Jan 20 2013

20 01 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):

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.

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.

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.

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.

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.

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

A review of the fossil record of ants.

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.

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.

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.

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.

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).

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.

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.

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 20th century’s biology that gave birth to the Modern Synthesis. Read the rest of this entry »





Top Research of 2012: Arthropods

26 12 2012

Jump to: Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.

Now that we’re done with the top books of the year, let’s look at the top research of the year. I re-examined a total of 412 papers published this year, sorted in the following categories: Arthropods; Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; and Zoology. As with the books, every day, I will do a top 10 research for each category. The top 10s will be inverted like a proper countdown. As with any top 10 lists, your mileage may vary; these picks and the rankings are all subjective and prone to my own biases.

Let’s start off with the arthropods. The top 10 papers were chosen from a master list of 74 papers. [OA] indicates open access papers. The topic listing, from 10 to 1: spider intelligence; spider silk; fossil insect behaviour; fossil pupation chambers; caste-specific neuroanatomy; early arthropod evolution; evolutionary dynamics; early fossil insect; earliest amber arthropods; treehopper helmet.


10. The discerning predator: decision rules underlying prey classification by a mosquito-eating jumping spider.

culi-oph

Jumping spiders’ excellent eyesight has led to their also having high intelligence, being able to observe and filter what they see to the point that the African jumping spider Evarcha culicivora can differentiate their prey, female Anopheles mosquitoes, from all other insects flying around just by looking at their antennae. This is what Nelson & Jackson showed with this elegant experiment.

By combining parts from male and female mosquitoes and using the resultant Frankenmosquitoes as lures for the spiders to attack, they identified the two clues that led to the most attacks: a red, blood-engorged abdomen, and slender antennae. Both of these are female mosquito features: male mosquitoes don’t feed on blood (they’re nectar feeders), and males have bushy antennae. As for the specificity for Anopheles mosquitoes, that’s explained by their posture – other mosquitoes rest with their body parallel to the ground, while Anopheles rest with a 45° angle.

For showing that such a tiny spider is capable of such complex prey-distinction and thus giving even more credence to the notion that intelligence is not a function of brain size, as well as for having a great experimental design, Nelson & Jackson get the #10 place.


9. Post-secretion processing influences spider silk performance.

Spider silk is not a simple strand that’s the same in every species. There’s many different types of silk that come out of different glands, and the silk is also modified after it’s secreted. The study focuses on major ampullate silk, the type of silk that makes up the framework of an orb web and whose stiffness is responsible for the strength of the webs. The researchers examined natural silk, and silk that they supercontracted to remove any post-secretion modifications. What they found was that these supercontracted silks lost the stiff properties of their natural counterparts, meaning that their properties come from whatever modification is made to them, not from the actual structure and composition of the silk. I find this discovery significant because it adds a new dimension to the study of spider silk, a field that has quite a lot of technological and biomimetic research ahead of it.

Other significant spider silk and web-related research this year include:

The role of capture spiral silk properties in the diversification of orb webs: how various silk types affect the web’s properties.

Nonlinear material behaviour of spider silk yields robust webs: This research provides more insight into the factors mentioned above, finding that it isn’t just the type of and modification of silks that affect the web’s properties, but that the geometry of the web is as important in determining its strength and behaviour.

Early Events in the Evolution of Spider Silk Genes [OA]: A phylogeny of genes from the silk-producing glands reveals gene duplications associated with more diverse ecological use of silk and webs.

Functional values of stabilimenta in a wasp spider, Argiope bruennichi: support for the prey-attraction hypothesis: research into the use of stabilimenta, UV-reflective strands of silk that orb-weavers have.


8. Jurassic mimicry between a hangingfly and a ginkgo from China. [OA]

gingko

This is cool more than anything else, and the mimicry is shown in the picture above, from the original paper: A, B, E, and F are gingko leaves; C and H are the described specimen and its wing, D and I are a closely-related species which also exhibits mimesis with gingkos; J and K are gingko leaf closeups. As you can see, the similarities are striking, and the artist’s conception in G shows how well the hangingfly would have blended in. The paper has more details on the coevolution of mimesis between this group of hangingflies and gingkos. In all, a neat piece of work with evolutionary insights as well as cool fossil preservation.

Another paper this year has preserved evidence of insect behaviour: Wing stridulation in a Jurassic katydid (Insecta, Orthoptera) produced low-pitched musical calls to attract females. The mating call of a katydid has been reconstructed based on the preservation of its stridulatory apparatus, a hard file that the wings strike against to make the music. Related, this paper from this year shows how sensitive the hearing of katydids is: Auditory change detection by a single neuron in an insect.


7. The Earliest Evidence of Holometabolan Insect Pupation in Conifer Wood. [OA]

xylokrypta

This paper describes U-shaped burrows in 210 Ma wood from Utah, USA. These were previously assumed to be bee or wasp borings, but the detailed analysis presented in the paper shows that these borings are actually pupation chambers made by a small organism that ate its way into the wood, then emerged from the other side, as presented in the diagram above. From the size of the borings, the authors propose that the organism is a cupedid beetle, showing that these beetles were dominant before the other beetles radiated later.


6. Division of Labor in the Hyperdiverse Ant Genus Pheidole Is Associated with Distinct Subcaste- and Age-Related Patterns of Worker Brain Organization. [OA]

pheidole_brain

That different castes will have a different brain organisation is expected and has been shown in many papers (e.g. 1, 2, 3). This paper is significant because it’s so thorough: it examines castes of three species of Pheidole ants and their brain anatomy. The diagram above summarises the pattern observed: the colours are species, the shapes are castes; the axes are two variables that together make up 87% of the brain variation seen. The pattern is clear: neuroanatomy is determined by caste, not by species. This is just underlines the incredible amount of plasticity in ants (and other eusocial insects), where the environment can dictate how an individual will function and develop to allow the colony to adapt to changing needs and conditions.


5. A Carboniferous Non-Onychophoran Lobopodian Reveals Long-Term Survival of a Cambrian Morphotype.

carbotubulus

This paper has equal relevance to palaeontology as it does to arthropods: like several other papers of the past few years (e.g.), it reinforces the idea that the Cambrian freaks didn’t go extinct, but that the nature of the fossil record changes since the Cambrian to make their preservation much rare (the advent of burrowing made it much harder for such soft-bodied forms to be preserved). This one is the most stirking example yet: a long-legged lobopod, 200 million years after the Cambrian (it comes from the famous Mazon Creek locality in Illinois, USA, 296 Ma)! Lobopods are a wastebasket taxon in which soft-bodied arthropods with stubby legs are dumped, including many fossil-only taxa, tardigrades, and onychophorans. There are two groups: short-legged forms (includes the last two) and long-legged ones, up until this paper known only from the Cambrian.

It was a good year for arthropod evolution, with many excellent studies into the biology and diversity of early arthropods:

Exceptionally preserved crustaceans from western Canada reveal a cryptic Cambrian radiation: These Canadian fossils bring the earliest fossil records of branchiopods, copepods, and ostracods back to the mid-Cambrian.

Silurian horseshoe crab illuminates the evolution of arthropod limbs: A horseshoe crab from Herefordshire, showing a very exciting biramous limb, the significance of which would need an entire post to explain.

A Silurian myodocope with preserved soft-parts: cautioning the interpretation of the shell-based ostracod record is another Herefordshire find that finds that ostracod shells, very abundant fossils with significant stratigraphic and other practical use, are not quite as informative taxonomically as previously thought.

Cambrian lobopodians and extant onychophorans provide new insights into early cephalization in Panarthropoda [OA]: A complete redescription of Onychodictyon‘s head, showing that the arthropod mouth may have originated multiple times.

Cambrian bivalved arthropod reveals origin of arthrodization: A new Burgess Shale arthropod suggests that the key feature of arthropods, the exoskeletal segmentation, was a feature that evolved for swimming.

Morphology of Cambrian lobopodian eyes from the Chengjiang Lagerstätte and their evolutionary significance shows that Cambrian lobopods had pretty sophisticated eyesight.

Complex brain and optic lobes in an early Cambrian arthropod: Eyes are nice and all, but how about preserved brains and nervous tissue?

Internal Soft-Tissue Anatomy of Cambrian ‘Orsten’ Arthropods as Revealed by Synchrotron X-Ray Tomographic Microscopy [OA] shows more spectacular internal details of long-extinct arthropods.

Exceptionally Preserved Cambrian Trilobite Digestive System Revealed in 3D by Synchrotron-Radiation X-Ray Tomographic Microscopy [OA]: As above.


4. Loss of flight promotes beetle diversification. [OA]

flightloss

In this study, a molecular phylogeny of Japanese carrion beetles was done, and the result found was that flight loss promotes speciation. Flightless populations have more genetic differences between themselves than do flight-enabled populations. This is to be expected: flight enables greater geographic dispersal, allowing distant populations to reproduce and keep gene flow between them; with flight loss, this doesn’t happen, resulting in more isolation and thus more speciation, as shown in the above bar chart. The authors went further and did a short meta-analysis for other beetle groups and found a similar effect. I look forward to deeper studies examining the precise interplay between diversification and flight loss – does flight loss really directly cause speciation, or is it an indirect knock-on effect. Loss of flight must be related to other factors such as habitat requirements, life history, or feeding preferences, as the authors note; maybe it’s those other factors that actually promote the speciation. The authors checked for this in their carrion beetle dataset, but it’s worth looking into with other taxa.


3. A complete insect from the Late Devonian period.

strudiella

The fossil doesn’t quite look like an insect until you examine it closely – when I first saw the picture, I thought it was some notostracan. But then it becomes clear that there’s a pair of antennae, then you see the head, then the rest of the body – this is an insect. It’s not the oldest – that honour remains with Rhyniognatha hirsti – but it does come from a time when the fossil record of insects is completely lacking, the Late Devonian, and it’s by far the earliest complete insect – this really is a landmark find.


2. Arthropods in amber from the Triassic Period.

triassicambermite

This is not the oldest amber (that’s from the Carboniferous), but it is the oldest fossiliferous amber. Microorganisms have been reported from it before, but this paper records the oldest arthropod inclusions in amber, beating the previous records from the Middle East by some 100 million years. The arthropods are one fly and two mites (one of which is pictured above), with more still to come in future papers.

Some more cool insect preservation papers published this year include:

The original colours of fossil beetles details how preservation of beetle cuticle allows us to reconstruct the colour of fossil beetles – after all, the metallic sheen that some beetles have isn’t due to pigments, but due to the nanostructure of the cuticle playing tricks with the light. THE CONTROLS ON THE PRESERVATION OF STRUCTURAL COLOR IN FOSSIL INSECTS outlines the details of how cuticle preservation affects recovered colour.

WIDESPREAD PYRITIZATION OF INSECTS IN THE EARLY CRETACEOUS JEHOL BIOTA shows that the insects from Jehol – the famous lacustrine fossil locality that has yielded many feathered dinosaurs – are pyritised with the help of bacterial acitvity.


1. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence. [OA]

helmet

In 2011, Prud’homme et al. published an intriguing paper with developmental and some morphological evidence that the helmet of treehoppers, pictured above, is actually a cooption of an ancestral wing-like structure. This is obviously a very extraordinary claim, and this paper reviews all the evidence and comes up with alternative scenarios that show flaws in the Prud’homme et al. paper. It gets the top spot not only for the subject matter, but also for being a prime example of the scientific method in action.

A morphology-only critique of the Prud’homme et al. paper was done very early in the year by Yoshizawa [OA].


Jump to: Botany; Developmental Biology; Ecology; Environmental; Evolution; Geology; Historical Geology; Human Evolution; Palaeontology; Zoology.





Most Interesting Papers of the Week

23 12 2012

Just because it’s 2012 in review time, doesn’t mean regularly-scheduled posts won’t go up!

These are papers that may be of general interest published this week, with commentary as necessary. No specific case studies, overly specialised research, or taxonomic papers. Papers ordered only by their appearance in my inbox. For PDFs, e-mail me, I get most of them. You can request an in-depth analysis of any paper and I’ll do it as I get the time.

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

17 papers this week, 7 of them open access.

New Books in the Store:

Special Issues:

This issue contains fairly specific review articles, all of which are excellent. Check out the titles and download whatever strikes your fancy to have a handy resource: they’re all [OA]!

This isn’t a named issue, but there are several papers, all [OA], dealing with the KT event. The must-have is Racki’s review, other wise there are two historical papers by Smit and Racki, and a series of end-Cretaceous ammonite papers for those interested, including a report of post-Cretaceous ammonites that’s pretty cool.

Several case studies and one good review, all [OA]

From the same journal issue as above come two specific papers on animal genomics and one review worth having, all [OA].

Arthropods:

Admittedly, this one has niche interest only. But it is the first time I see clades referred to as “epic”, and I think internet lingo really ought to bleed more into the scientific literature to lighten things up. Also, the phylogeny presented in here is very intriguing. It’s piqued my interest anyway.

A contentious paper, judging from the abstract. I haven’t gotten around to reading it yet though, so I cannot make any critical commentary besides stating my biases. I have a bad feeling about the idea that arthropods arose in the Precambrian, as all other papers that suggested this have been shit, no matter how sophisticated their methodologies. I have no problem with 3 independent colonisations of land. The evolution of insect wings much earlier than the fossil record indicates is also fine, but given that we already have flying insects in the Silurian, even before great sprawling forests, I fail to see when exactly they mean. But this all empty judgement; I haven’t read the paper, only the abstract with too little details on their methods and results.

Botany:

I gave an overview of the origin of angiosperms (flowering plants) in this post. Tl;dr version: the earliest angiosperms had very quick life cycles and so grew faster than the other plants of the era, and so managed to outcompete them in most environments. This happened in the Cretaceous. This paper provides more detail with a fossil-based temporal framework for the radiation of angiosperms:

These megafossil data demonstrate that angiosperms migrated into new environments in three phases: (i) Barremian (ca. 130–125 Ma) freshwater lake-related wetlands; (ii) Aptian–Albian (ca. 125–100 Ma) understory floodplains (excluding levees and back swamps); and (iii) Cenomanian–Campanian (ca. 100–84 Ma) natural levees, back swamps, and coastal swamps.

Some more corroboration of the ANITA/palaeoherb model outlined in the post I linked above.

Developmental Biology:

The neural crest, a developmental innovation that is the key to vertebrate success, is now known to have precursors in non-vertebrate chordates. Examining these gives crucial insight into its evolution. Read this paper in conjunction with the comprehensive phylogenetic overview of Hall (2008).

A complete review of the development of the vertebrate heart:

Organogenesis of the vertebrate heart involves a complex sequence of events initiating with specification and differentiation of myocardial and endocardial cells in anterior lateral mesoderm shortly after gastrulation, followed by formation and rightward looping of the early heart tube. During looping, the heart tube elongates by addition of second heart field progenitor cells from adjacent pharyngeal mesoderm at the arterial and venous poles. Progressive differentiation is controlled by intercellular signaling events between pharyngeal mesoderm, foregut endoderm, and neural crest-derived mesenchyme. Regulated patterns of myocardial gene expression and proliferation within the embryonic heart drive morphogenesis of atrial and ventricular chambers, while cardiac cushions, precursors of the definitive valves, form in the atrioventricular and outflow regions. In amniotes, separate systemic and pulmonary circulatory systems arise by septation and remodeling events that divide the atria and ventricles into left and right chambers. Cardiac neural crest cells play a key role in dividing the arterial pole of the heart into the ascending aorta and pulmonary trunk. During the remodeling phase the definitive cardiac conduction system, that coordinates the heartbeat, is established. In addition, the epicardium, critical for regulated ventricular growth and development of the coronary vasculature, spreads over the surface of the heart as an epithelium from which cells invade the myocardium to give rise to diverse cell types including fibroblasts and smooth muscle cells. Cardiogenesis thus involves highly coordinated development of multiple cell types and insight into the different lineage contributions and molecular regulation of each of these steps is expanding rapidly.

Homeobox genes are the coolest genes there are. They are transcription regulators that play key roles in multicellular development. The most well-known are the HOX genes of animals, genes which pattern the embryo (change the HOX genes around and you can make mutant flies with legs instead of antennae, for example). This review focuses on the historical evolution of animal homeoboxes, but it’s very comprehensive in that respect.

The most important factor in brain power isn’t brain size, it’s the number of connections in and between the brain sections, in other words the density of the networks. This review examines how the cerebellar network develops.

Two primary germinal zones generate the cells that make up the cerebellum. Each zone expresses a specific set of genes that establish the cell lineages within the cerebellar anlage. Then, cohorts of differentiated projection neurons and interneuron progenitors migrate into the developing cerebellum. Thereafter, a number of remarkable patterning events occur including transformation of the smooth cerebellar surface into an intricately patterned series of folds, formation of three distinct cellular layers, and the demarcation of parasagittal gene expression domains. Together, these structural and molecular organizations are thought to support the proper connectivity between incoming afferent projections and their target cells. After birth, genetic programs and neural activity repattern synaptic connections into topographic neural networks called modules, which are organized around a longitudinal zone plan

Evolution:

I love Yokoyama’s lab’s work – it’s this work that I talk about in the last paragraph of my photorecption in animals post, using phylogenetics to reconstruct the visual pigments of ancestral animals and putting them into modern animals to see how those extinct animals would have viewed the world. Yokoyama reviews the full scope of their work, beyond this cool stuff as well. It’s all very interesting, and prime examples of innovative research in my opinion.

Much like caves, ancient lakes are some of the most sought-after environments for evolutionary research, because the animals in them are isolated for enough generations for the effects of evolution to be documented step-by-step in the wild. All the research on the awesome cichlid radiations in Tanganyika is an example of ancient lake research; I wrote on a classic fossil ancient lake, the Steinheim Basin, back in the baby days of the blog. This paper reviews the evolution of molluscs in ancient lakes of the Malawi Basin, which includes Lake Tanganyika and Lake Malawi.

An excellent example of convergent morphological evolution arising from a shared molecular basis. The study organisms are Drosophila ezoana and D. sechellia, two species that diverged from each other 40 million years ago. They both share a convergently evolved trait of having a hairless larval cuticle, due to the downregulation of Shavenbaby, a developmental gene whose expression allows hair growth (the hairs are called trichomes). This paper finds that the mutations behind this downregulation arose independently in these two distant species, leading to the same derived phenotype.

A great review paper outlining the ubiquity and evolutionary importance of symbiosis in animals.

Historical Geology:

This paper shows that unlike the usual portrayal (including by me!) of the P-T extinction as an event that so devastated life that it took it 30 million years to recover properly, the delayed recovery was actually caused by the early Triassic climate being cold and uneven – the recovery and repeaking of biodiversity occurred coincidentally with a return of a warm climate.

This is actually something I went into several months ago in a public lecture I gave about extinction rates (not up on the blog yet due to time constraints): extinctions are rarely singular events, and the P-T is not one of the exceptions. Here, it’s found the the extinction actually went on further than the P-T boundary, with a second extinction occurring in the earliest Triassic:

The first stage of extinction occurred during the latest Permian, and was marked by the extinction of 57% of species, namely all plankton and some benthic groups, including algae, rugose corals, and fusulinids. The second phase occurred in the earliest Triassic, and resulted in the extinction of 71% of the remaining species. This second extinction phase fundamentally altered the marine ecosystem structure that had existed for the previous 200 million years.

Human Evolution:

A surprising result here: the lightening didn’t take place as soon as the Out of Africa migration, but underwent two phases, one after Out-of-Africa and another 11-19 thousand years ago, the discrepancy caused by the multitude of genes involved and the fact that it took a while for human populations to expand enough for naturals election to start acting strongly enough to favour the light-skin variants.

Palaeontology:

A new amazing example of exceptional preservation. Not only is finding a 200 Ma fossil leech cocoon awrsome on its own, further examination revealed a ciliate inside its wall, in other words a preserved unicellular protozoan. Not just some hint of a ciliate either, it was preserved in such detail that it can be identified as a peritrich:

The microfossil consists of a helically contractile stalk that attaches to a main body with a peristomial feeding apparatus and a large C-shaped macronucleus. It agrees in every aspect with the living bell animals, such as Vorticella. Vorticellids and similar peritrichs are vital constituents of aquatic ecosystems worldwide, but so far have lacked any fossil record.

Zoology:

A review of animal sentience, with a focus on animal rights and welfare.





Most Interesting Papers of the Week

9 12 2012

These are papers that may be of general interest published this week, with commentary as necessary. No specific case studies, overly specialised research, or taxonomic papers. Papers ordered only by their appearance in my inbox. For PDFs, e-mail me, I get most of them. You can request an in-depth analysis of any paper and I’ll do it as I get the time.

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

12 papers this week, 4 of them open access.

New Books in the Store:

Special Issues:

“Evolutionary rescue” happens when a population or species becomes adapted to environments which are lethal to its ancestors. This special issue is full of case studies and examinations of the phenomenon from a theoretical level, so worth reading if this interests you. Schiffer et al. is the only [OA] paper, luckily it’s one of the more interesting ones.

An amazing special issue on one of the coolest phenomena in biology, one which I’ve written about before: parasites that take over and manipulate their hosts’ behaviour. All the papers here are excellent reviews.

If you’re even remotely interested in human evolution, get the papers from this special issue. They cover everything, from development in hominins to morphology to brain to language and ecology. Very highly recommended.

Botany:

Given just how dependent on physical factors plant development is, it’s no wonder that they develop somewhat differently in space with no gravity. This research is cool because it allows us to narrow down exactly what is gravbity-dependent and what isn’t. Besides this, it’s also useful in case we ever get around to establishing space colonies or something.

Evolution:

An introduction to caves as ideal nmatural arenas for evolution isn’t needed. This paper demonstrates that in caves, evolution will be canalised to form distinct morphological classes, and that the emergence of these classes is dependent on the cave habitat to which a species is adapting. That this happens for the entire community is the remarkable result, meaning that these morphologies are ecomorphs, not just specific adaptations. Of course, this study was only done with one genus, but the same result being found with a broader taxonomic study wouldn’t surprise me.

This is what I would love to do if I had money and a lab.

History:

This is an excellent look at the history of ideas about speciation, and also serves as a glossary/dictionary. Worth keeping just as a reference.

Microbiology:

This is of interest for those who are into endosymbiosis.

Palaeontology:

Amazing find that will require me to update my stock history of life lecture, specifically the part that says that the only mammals that survived past the KT event were marsupials and placentals. This Miocene fossil is a mammal and is neither a marsupial nor a placental. Okay, I’m overblowing it a bit, since apparently this has been known for a bit, but it’s the first I’ve heard of it (and I consider myself as keeping abreast of the literature). So, still spectacular.

This is significant for those interested in the evolution of birds.

Here, we redescribe the wings of the archaic bird Archaeopteryx lithographica and the dinosaur Anchiornis huxleyi and show that their wings differ from those of Neornithes in being composed of multiple layers of feathers. In Archaeopteryx, primaries are overlapped by long dorsal and ventral coverts. Anchiornis has a similar configuration but is more primitive in having short, slender, symmetrical remiges. Archaeopteryx and Anchiornis therefore appear to represent early experiments in the evolution of the wing. This primitive configuration has important functional implications: although the slender feather shafts of Archaeopteryx and Anchiornis make individual feathers weak, layering of the wing feathers may have produced a strong airfoil. Furthermore, the layered arrangement may have prevented the feathers from forming a slotted tip or separating to reduce drag on the upstroke. The wings of early birds therefore may have lacked the range of functions seen in Neornithes, limiting their flight ability.

Phylogenetics:

It never ceases to surprise me that this isn’t straightforward and clear. Remember: fossils provide the only tangible evidence for how traits evolved. They’re the baseline information against which everything else must be checked for validity.

Zoology:

In zoology, “gordian knot” refers to an aggregation of mating nematomorphs (hairworms) – the normally free-living aquatic organisms gather into a tight ball, imaginarily reminiscent of Midas’s legendary knot. This study looked at what exactly happens in these Gordian knots. I was surprised that the knots are first composed entirely of males, with females getting in the mix later.

I mentioned chemosynthesis in the deep sea in two of my deep sea posts. This paper is a thorough review, concentrating on those organisms that can survive solely by chemosynthesis and not rely indirectly on photosynthetic products, like oxygen or marine snow.

This paper has a ton of coauthors and it’s not a genomic paper? Expectations are automatically raised then. And it doesn’t fail – it serves as a standard reference for how many marine species have been described so far. I will need to read the statistics for how many exist in total more carefully as I’m a bit skeptical of the number they predict (0.7 – 1 million) – it seems rather low to me. Still, get it if you’re interested in biodiversity.

The neural crest has long been considered the key innovation that allowed vertebrates to achieve their evolutionary success. Some authors even go as far as treating it as a fourth germ layer. Basically, the neural crest is a dorsal fold of the neural tube from which a population of migratory multipotent cells is derived. These migrate along specific pathways to form, among other things: the skull and face, teeth, a lot of the heart and circulatory vessels, pigment cells, the spinal column and the peripheral nervous system, and the thyroid and adrenal glands.It’s also long been known that its evolution was not a spontaneous one, but that glimmers of it can be seen in other chordates. This paper is significant in that it identifies more than “glimmers”: it identifies a full-fledged neural crest in a tunicate.





Most Interesting Papers of the Week

25 11 2012

These are papers that may be of general interest published this week, with commentary as necessary. No specific case studies, overly specialised research, or taxonomic papers. Papers ordered only by their appearance in my inbox. For PDFs, e-mail me, I get most of them. You can request an in-depth analysis of any paper and I’ll do it as I get the time.

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

18 papers this week, 2 of them open access.

New Books in the Store:

Special Issues:

I was mostly interested in McInerny & Etienne.

All papers [OA]! I especially recommend Dunn et al. and Telfer & Bown.

Arthropods:

Every aphid species has special cells called bacteriocytes within which live symbiotic bacteria, Buchnera. This relationship has been around for ~250 million years, and is retained because it’s an obligate symbiosis for both the aphid and the bacterium, since neither can reproduce successfully without the other. This paper identifies just how deep the co-speciation has gone between these two is, with aphids generating completely new proteins to deal somehow with Buchnera:

We identified a novel class of genes that encode small proteins with signal peptides, which are often cysteine-rich, that are over-represented in bacteriocytes. These genes are first expressed at a developmental time point coincident with the incorporation of symbionts strictly in the cells that contribute to the bacteriocyte and this bacteriocyte-specific expression is maintained throughout the aphid’s life.

This is a thorough review of Mesozoic weevils. If you work with them, get it! For the basics of weevils, see my post.

Botany:

This review summarizes current knowledge about optimal defence patterns in above- and below-ground plant tissues, including information on basal and induced defence metabolite accumulation, defensive structures and their regulation by jasmonic acid (JA).

“Floral mimicry” refers to traits in flowers that allow them to attract insects by mimicking other flowers in either Batesian (mimic offers no nectar reward) or Müllerian (both flowers mimic each other, resulting in more flower visits to both) ways. This study shows which traits are most important for flowers to mimic, at least in orchids.

This study shows that traits that mimic, in order of importance, the spectra, shape and nectar guide patterns of flowers of rewarding plants would be under strong selection in food-deceptive orchids as they maximize attractiveness to their pollinators.

One of my pet peeves is the overreaction to wildfires, with people exclaiming that they’re disastrous to ecosystems. No, they’re not. Plants in wildfire-prone areas are adapted to seasonal fire, and adaptations to fire are ancient in many plants, as this paper demonstrates.

Focusing on the widespread 113-million-year-old family Proteaceae, fireproneness among Gondwanan Angiosperm floras can now be traced back almost 90 million years into the fiery Cretaceous. The associated evolution of on-plant (serotiny) and soil seed storage, and later ant dispersal, affirms them as ancient adaptations to fire among flowering plants.

Environmental:

A good meta-analysis on the topic.

We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations.

Evolution:

Besides being a good review of the state of the art, this is an excellent reference article:

I also provide tables with full or summarised data on (a) genital asymmetry across all animal phyla with internal fertilisation; (b) genera with dextral as well as sinistral species; (c) species with dextral as well as sinistral individuals; (d) genera with symmetric as well as asymmetric species; (e) species with symmetric as well as asymmetric individuals.

(Historical) Geology:

The break-off of India from Gondwana and its subsequent crash into Asia, forming the Himalaya Mountains, is one of the most spectacular events in Earth’s history – the Himalayas changed climatic conditions (including setting the stage for human evolution!), and the sheer speed at which India jetted into Asia is remarkable. There’s even speculation that it may have played a role in the Cretaceous extinction, since its path went through the Reunion magmatic hotspot, where India might have picked up the lava that later went into the Deccan Traps. This reviews deals with how India evolved during this time.

A geochemical analysis of the most important Chinese Ediacaran localities (including Dengying and Doushantuo), with implications for palaeoenvironment. See Bristow et al. (2009) for more information.

Palaeontology:

Phosphatocopines are a group of 60+ Cambrian bivalved arthropods (probably crustaceans) with a unique, phosphatised carapace.

Not all impacts are globally-devastating events.

I didn’t know people still wrote Cenozoic like that.

The earliest flying fish fossil!

Zoology:

Cool party trivia.

I wrote about this cancer and its detrimental effect on the Tasmanian Devil in this post (the charity offer is long gone by now, although you should still buy that book anyway).





Q&A with me about my favourite entomological research

22 10 2012

A colleague of mine who teaches entomology at a university in France invited me last week to talk with one of his MSc. classes about life, the universe, and everything. We skipped the universe part because astronomy is boring, but the conversation on life – and the study of it – was pretty interesting. Among other things, their questions were centered about what kind of feasible research I find to be valuable – the goal of the exercise was to help them in finding their way in their research theses and their academic future.

Since the conversation was all in French, I didn’t bother recording it for the blog, but here is an abridged transcript of a couple of parts from the Q&A of general interest. Other questions were about my own research and experiences from doing academic research while not being in academia. In all, the Skype session lasted ~20 minutes, with 5 minutes of introduction. Quick and dirty, only meant to take up half the lesson time because their literature session didn’t have that much literature in it that week.

What insect neuroscience research would you do if you had a lab with unlimited funding?

As far as I know, currently, all studies on insect neurology concern what happens when an insect is doing a specific action – foraging bees looking for a target, moving legs, chemical stimulation, that sort of thing. These are ineresting in their own right, of course, but I would personally find some value in finding out how the neuronal machinery is acting when the insect is at rest, not seeking to fulfil any particular goal or task. This has been a recent development in human neuroscience at least – they call it research into the “default-mode brain” – and the insights from it could serve us well in finding out about the general cognition of insects.

What are some ways in which our knowledge of individual insect ecology can be furthered without using fancy technology, but also without hours of observations in the field or lab?

That seems like a utopian wish, I can’t really think of much. One thing that comes to mind could be architecture and integrating it with physics. For example, I work a lot with the ecology of larval antlions and their pit traps, and some of my results include that contrary to what is normally found, the size of the antlion pit doesn’t necessarily correlate to hunger level. Whether this is a fluke or not, I don’t know, but what I can also hypothesise is that simply measuring diameter is insufficient. We know that the substrate that antlions are digging in also has an effect, and we know that antlion traps are very precise constructs, with the slightest disturbance by an ant causing it to collapse. This is because of the contouring on the perimeter of the pit, which can very easily and precisely be measured with a pinhole camera and some hours spent programming. This is just an idea kicking around in my head involving shadows (I did somewhat similar work when working with µ-CTs), but it should be feasible to get a precise topography of the pit perimeter. Integrating that with some physics will give us a very good view of just how the antlion pit works and how that flows into their ecology.

Which taxonomic group would you like to see more work done on?

I will have to say staphylinids. They’re the most diverse family of insect, but their identification even to subfamily level is pretty hard, or so I find. The literature, including keys, is also fairly scattered. If anyone can make a good comprehensive regional species key for the Eastern Mediterranean, I’d be eternally grateful, especially since staphs are one of the more important forest ecosystem components, and the bulk of my entomological research here takes place in forests.

What is your favourite research program taking place nowadays?

I love the wrk that’s being done with the evo-devo of wing patterns in butterflies. It’s an excellent system for investigating all the levels of macroevolution, from the genetic underpinning of novel features all the way through to their effects on fitness through ecological success, especially when it comes to eyespots which are used to deter predators. This research is going to provide all the insights needed for the new evolutionary synthesis that’s coming to supersede the Modern Synthesis.

What about when the research has to involve botany?

The research about how plants reacts to eggs and larvae. I especially liked a study from a couple of years ago that showed that Pieris brassicae eggs can cause the host plant to release chemicals thatsuppress the plant’s defensive system, thereby allowing the caterpillars free access to the plant. It’s hilarious. And also a very cool research topic.





Interesting Papers of the Week

14 10 2012

These are papers that may be of general interest published this week, with commentary as necessary. No specific case studies, overly specialised research, or taxonomic papers. Papers ordered only by their appearance in my inbox. For PDFs, e-mail me, I get most of them. You can request an in-depth analysis of any paper and I’ll do it as I get the time.

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

13 papers this time, 5 open access.

Index:


Special Issues:

It’s not really a special issue, but it’s best to classify any volume of this here. These are biographies of recently dead Royal Society members (“recently” measured in a timespan of years). Most interesting to me in this issue was Harry Whittington’s, the driving force behind the reinterpretation of Burgess Shale fossils in the 1970s and dead in 2010. Other biologists featured in this volume: Seymour Benzer (genetics); Tony James (biochemistry); Arthur Kornberg (biochemistry); Dan Lewis (botany); Iain MacIntyre (endocrine systems).


Arthropods:

I’ve always supported a placing of the tardigrades as very close to the arthropods. Nice to see some more support.


Developmental Biology:

Gastrulation is the time of development when the germ layers are established. The majority of animals, excluding cnidarians and sponges, have three germ layers: endo-, ecto-, and mesoderm. Endoderm is responsible for things like the digestive system and lungs; ectoderm is responsible for the nervous system; and mesoderm for muscular and skeletal systems. This review outlines the steps that happen during gastrulation.

Because they’re immobile, plant physiology is fascinating – unlike animals, they have to face changing environmental conditions head-on, they can’t migrate or hide. They’re thus very flexible, with this flexibility caused by their continuously having populations of stem cells allowing plants to develop through their entire life cycle, as dictated by hormones. These hormones are reviewed in this paper. See Farnsworth (2004) for an ecological perspective.


Ecology:

I don’t quite agree with the conclusion of this paper, that deep sea habitats are evolutionarily stable. As I wrote in my deep sea posts, there is an equal amount of evidence suggesting that animals can recolonise the deep sea multiple times as environmental changes dictate. This doesn’t precluse some organisms truly being deep sea specialists though. In all, I would say that there is no generalisation.


Environmental:


Evolution:

Cave animals are some of the best examples to use of evolution. If you’re teaching evolution, get this paper for very thorough reviews of two cavernicolous model organisms, showing what happens to organisms when they’re left to evolve in the perpetual darkness of a cave: the fish Astyanax mexicanus and the isopod Asellus aquaticus.


History:

Those who’ve been reading the blog since the beginning will remember one of the earliest post series, on the planorbid snails of the Steinheim Basin (part 1 and part 2). I also mentioned the snails in my natural selection post. I really don’t know why Hilgendorf’s work is not more generally well-known – no popular evolution books mention them, to my knowledge, and it’s a shame because this isn’t only historically significant as the very first published evidence of gradual evolutionary transitions from only the fossil record and one of the first explicit phylogenetic hypotheses, but it’s a pretty good example of those too. I think one of the main reasons is that it’s from Germany; hopefully this paper will go some way to rectify the situation, providing a translation of Hilgendorf’s original dissertation as well as reviewing his corpus of related work.


Palaeontology:

The preservation here is stunning. Fuxianhuia is one of the more disputed arthropods of the early Cambrian due to its possession of “great appendages”, but making the “great appendage” arthropods paraphyletic. It’s classified as a stem-group euarthropod. Thus, the findings presented in this paper are very surprising: its brain shares many similarities with malacostracan brains, despite Fuxianhuia decisively not being a crustacean. It’s quite intriguing – not the fact that Fuxianhuia has a highly-developed brain (that’s a given), but the fact that the developments are so strikingly similar. To me, it means we have to be somewhat more careful with neurophylogenies – some characters may be very ancestral without our recognising them. I hope more stem-group arthropods get this same treatment (I can’t wait to see the brain of Anomalocaris).


Zoology:

Hapalochlaena lunulata is the greater blue-ringed octopus and the primary reason to not go swimming in Australia – it’s highly-poisonous and lives both in reefs, and shallow inlets and bays (i.e. no place is safe, although to be honest, they aren’t aggressive). The blue rings are chromatophore rings that are flashed as warning colouration, mostly to deter predators. They also flash them when feeding, after mating, and when under physiological stress. This paper describes the mechanism behind the flashing.

Thermoregulation. Specifically, the hair helps them lose heat – a complete flip from the usual insulatory function of hair. Interesting stuff.





Top Papers of the Week: 23.01-29.01.2012

30 01 2012

The master list for this week is here. Only those categories with more than one paper will be considered. Taxonomy will be exempt, because new species descriptions isn’t the kind of thing I can choose between. Read the rest of this entry »





Weekly Research: March 21-27, 2011

28 03 2011

Read the rest of this entry »








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