Spider Vision

27 04 2013

This is a requested post on the basics of spider eyes; for more on spiders, check out my spider lecture.

Spiders only have ocelli, simple eyes consisting of a lens covering a vitreous fluid-filled pit with a retina (pigment cells + visual cells) at the bottom. The ocelli come in two types: the main eyes and the secondary eyes.

Eyes in spiders are named after their respective position on the head. Therefore, we distinguish between the following:

  • Anterior median eyes: front, center;
  • Anterior lateral eyes: front, side;
  • Posterior median eyes: back, center;
  • Posterior lateral eyes: back, side.

The anterior median eyes (AMEs) are always the main eyes, present in all spiders except the Dysderidae, Sicariidae, and Oonopidae. You can easily recognise them in pictures because they’re black, a consequence of not having a tapetum that reflects light back out. Main eyes are fairly uniform in all spiders and differ in their structure from secondary eyes in that they’re everted eyes – the light-sensitive parts of the retina (the rhabdomeres) are pointed towards the light.

All the rest of the eyes are secondary eyes. Secondary eyes are inverted, with their rhabdomeres pointing away from the light, same as in vertebrates (including the human eye). The number and arrangements of secondary eyes can differ significantly, as can their structure: for example, a typical garden spider has lateral eyes with a tapetum, while median ones lack it. All of these differences mean that secondary eyes are incredibly useful for taxonomic purposes, and it’s often so that merely looking at the eyes of a spider will give you a reliable identification of its family.

These differences result in highly-variable image qualities, and have most probably evolved due to ecology. Large secondary eyes can contain several thousand rhabdomeres, resulting in very high sensitivity to light that is very useful to hunters and/or nocturnal spiders. In contrast, small secondary eyes contain a couple hundred rhabdomeres at best, rendering them fairly useless for much beyond movement detection, which is why web-building spiders tend to have them: they don’t need fancy eyes for hunting.

Main eyes are immobile, small, and have a short focal length, granting the spider a large depth of field, making it unnecessary for them to have a focusing mechanism for short ranges. The best main eyes are found in salticids and thomisids, where they are enlarged, resulting in a clear, crisp picture.

This pictures is then combined with the 3D perspective given by the mobile and widely-spread secondary eyes in order to allow the spider to judge distances, most useful for hunting or ambushing spiders.


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Reading List: Human Evolution papers

20 04 2013

The following is the reading list I would give to a typical undergraduate human evolution course. The purpose is not to give the students papers with the descriptions of every new fossil species (a perusal of Wikipedia can get you all their names), but to provide a comprehensive overview of the breadth of human evolution research beyond the palaeontology, as well as general reviews that may be dated – a critical skill for any science student is to be able to dig out advances that have happened since the publication of a paper and put these advances within the general research context.

Sorted alphabetically by author, not by importance. Links lead to abstracts, privately-hosted PDF links also included. You can batch download all papers from this Dropbox folder. Also check out the listing of recommended books on human evolution.

Papers:


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Categories : Vertebrates, Zoology

Reading List: Human Evolution books

20 04 2013

These are scientific books about human evolution I always recommend. The target audiences run the gamut from academics to lay public, all are dumped together.

Sorted alphabetically by author name. Also check out my human evolution reading list for undergrads.


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Categories : Books, Vertebrates, Zoology

Bryozoan Placentas

4 04 2013
Celleporella hyalina. Source.

Celleporella hyalina. Source.

Pictured above is Celleporella hyalina, a species of cheilostome bryozoan. Bryozoans are aquatic, filter-feeding, colonial organisms – each opening up there is the house of an individual bryozoan, and they all live together in this colony that can sprawl over any substrate, often playing a significant role as foulers. Each house is technically called a zooid, and they’re made of calcium carbonate.

I bring them up because I got an e-mail asking whether any animals other than mammals have a placenta. In terms of the actual organ, no, the mammalian placenta is unique. But organs that serve the same function as the placenta do exist in some other animals, such as some bryozoans.

In bryozoans, fertilised eggs are kept in a special, fortified chamber, the ovicell, within the mother’s zooid. You can consider this like a womb. The ovicell has a door, the ooecial vesicle, that closes the ovicell off once implantation occurs – this protects the eggs from seawater.

Ovicell longitudinal section. Source.

Ovicell longitudinal section. Source.

In some bryozoans, the ooecial vesicle becomes enlarged as a special structure forms from its mother-facing wall: the embryophore. The light microscope picture above shows a longitudinal section through an ovicell. em is the embryo, eph is the embryophore; not shown to the right is the maternal zooid.

The embryophore keeps growing larger as the embryos grow, and its function is to pass on nutrients from the maternal zooid to the embryos in the ovicell. Therefore, we term it a placental analogue.


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Fossil Bone Histology

3 04 2013

9780520273528This is a brand new book by Padian & Lamm, published just last month by University of California Press: Bone Histology of Fossil Tetrapods: Advancing Methods, Analysis, and Interpretation. I have not read it (although it seems like a state-of-the-art book), but thought this would be a good way to introduce a basic post on fossil bone histology.

Histology is a widespread method in biology. At its purest, it’s the practice of slicing structures thin enough that we can shine light through them, making them examinable under a microscope. More advanced histology can involve staining to make certain components stand out. One can also make serial thin sections, scan them digitally, and make 3D reconstructions that can be navigated through.

Histology is also used in geology – making thin sections of rocks is the most surefire way of identifying their mineral components. All three-dimensionally preserved fossils can also be studied histologically – see my post on the Herefordshire locality for examples of fossils that can only be studied by serial histology.

Histology of fossil bones has a long history, dating back at least to the 19th century. See the work of James Bowerbank (1848) for an example using pterosaur bones. Much information can be gleaned from bone histology. For another pterosaur example, de Ricqlès et al. (2000) used histology to find that pterosaurs had a fast metabolism and grew at rates more similar to birds than to reptiles.

Such insights can then lead to more informed hypothesising about the ecology and systematics of extinct animals. For example, histological analyses of theropod bones show that they had bones that they grew very rapidly and with a structure typical of today’s large birds (Erickson et al., 2001); this is one more piece of evidence for the dominant hypothesis of birds being theropods.

The detail that can be received from such analyses is considerable. Varricchio (1993) found that the troodontid dinosaur Troodon formosus reached its adult size in less than five years. The basis for such observations is the fact that bone is a living tissue that records the growth and life of the animal. Bone deposition can occur in seasonal cycles, in which case the histological section shows a tree ring-like pattern, or bone deposition can be continuous. The rapidity of bone deposition results in different bone microstructure, all of it preserved in fossils, allowing easy distinction between fast and slow growth. In essence, you can make a cross section of a bone and read the story of its animal from birth to death, like a timeline. Below you can try it for yourself, using a diagram ripped from Martin’s Introduction to the Study of Dinosaurs (2006, 2nd ed.).

histolog

Starting from the bottom, you have a dark brown line. This is a line of arrested growth (LAG), a line indicating that no growth happened for a certain period. Between the first two LAGs are two closely-packed layers of fibrolamellar bone, characterised by those large white blotches, which are canals. These form when growth rate is high, so fibrolamellar bone is a telltale sign of fast growth.

Between the second and third LAG are two vascularised layers, but there is a distinct space between the layers. This is called an annulus, and the lack of canals tells us that the rate of growth was low.

So, taken all together, what this particular section shows us, generally, is a cyclical growth pattern. LAG, followed by vascularisation, annulus, vascularisation, then another LAG. One could take LAGs to represent yearly lines (as with tree rings), and the alternating vascularisation to represent seasonal cycles of fast/slow growth, and then hypothesise as to how these patterns can emerge. Hypotheses can then be tested somewhat using Recent bones with known growth patterns.

One can then go further and examine differences between growth patterns in adults and juveniles, provided specimens of the same species are around. This allows us to elucidate life history patterns – is there a fast juvenile growth rate then arrest, or did the animal grow at the same rate until death?

I can only offer you this glimpse into this research area, and my aim was not only to introduce it, but to give you an idea of how all the conclusions we come to about dinosaurs, their physiologies, their lifestyles, their ecologies, etc. aren’t baseless speculations, but come from detailed examination and analysis of such things as slices of fossilised bone. As the old palaeontologist adage goes, “every fossil tells a story”.

References:

Bowerbank JS. 1848. Microscopical Observations on the Structure of the Bones of Pterodactylus Giganteus and other Fossil Animals. Quarterly Journal of the Geological Society 4, 2-10.

De Ricqlès AJ, Padian K, Horner JR & Francillon-Vieillot H. 2000. Palaeohistology of the bones of pterosaurs (Reptilia: Archosauria): anatomy, ontogeny, and biomechanical implications. Zoological Journal of the Linnean Society 129, 349-385.

Erickson GM, Rogers KC & Yerby SA. 2001. Dinosaurian growth patterns and rapid avian growth rates. Nature 412, 429-433.

Varricchio DJ. 1993. Bone microstructure of the Upper Cretaceous theropod dinosaur Troodon formosus. Journal of Vertebrate Paleontology 13, 99-104.


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Top Research of 2012: Zoology

7 01 2013

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

Last but not least, my picks for the top 10 zoology papers of the year, with the caveat that I took the majority of stuff I follow, because nobody is really interested in the ultrastructure of annelid sperm-producing cells. So the papers listed here have some sort of general appeal, or so I hope. The revised master list contains 42 papers. [OA] indicates open access papers.

10. How does the blue-ringed octopus (Hapalochlaena lunulata) flash its blue rings?

Everyone’s at least heard of the blue-ringed octopus, famed for its deadly toxicity. Like most venomous animals though, they advertise it using the name-giving blue rings, of which there are 60. When threatened, the octopus flashes them to produce blue iridescence. Octopi have two ways to produce colour: iridophores, cells with plaques that reflect light in wonky ways; or chromatophores, sacs which produce colours chemically with pigments. This paper finds that the blue rings are made by iridophores, but with a twist: the iridophores aren’t just found on the surface, they’re integrated into special skin pouches. So when under threat, the muscles will automatically contract, turning the iridophores on mechanically. This contraction will also cause brown chromatophores to form a ring around the iridophores, thus increasing the intensity of the blue. This is also why the blue-ringed octopus flash is so extremely quick: it takes 1/3 of a second for the flash to be produced, and the speed is due to this smart mechanical system.

9. The erection mechanism of the ratite penis.

Just catering to fellow fans of juvenile humour. Although, to be fair, bird penises are fairly interesting, as exemplified by the explosive erections of ducks.

8. A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. [OA]

cephalophylo

This paper presents a phylogeny of the cephalopods. It’s fairly comprehensive with 188 species and only a handful of families missing, and the topology doesn’t contradict previous research. The authors then plotted 6 characters and did ancestral trait reconstructions, as seen above, where coliur represents presence, white repesents absence, and black represents unknown. From left to right, these are: accessory nidamental gland; cornea; autogenic photophore; bacteriogenic photophore; branchial canal; and right oviduct. On the right, they did the same but with depth: grey represents benthic lifestyles, white are pelagic, and black is unknown. This exercise gives two main results, which you cans ee for yourself as well: in the evolution, cephalopods moved a lot between habitats, and with the shifts followed many convergent losses and gains of certain traits.

Speaking of evolution of depth preferences in cephalopods, Vestigial phragmocone in the gladius points to a deepwater origin of squid (Mollusca: Cephalopoda) looks at the gladius of squid and homologises it with fossil belemnite features, which, together with the decalcification of squid, hints at a deep water origin of squid.

7. An Asian Elephant Imitates Human Speech. [OA]

speakingelephant

An elephant that can speak Korean. No kidding. Check the B graph above, and you’ll see that this male Asian elephant can pretty much identically imitate the frequency of the respective vowels. The imitation is so good that Koreans can understand and transcribe what the elephant is saying. It won’t be long until they can start understanding nuclear weapon schematics, and knowing the aggression of elephants, that’s not a good thing. Be afraid, everyone.

If, for some strange reason, you have an affinity for elephants, then you’ll be interested in What Is the Use of Elephant Hair? [OA] for giving you the answer to that titular age-old question. Spoiler alert: it helps with heat loss, something that elephants need to sustain their size.

6. Evolution of the turtle bauplan: the topological relationship of the scapula relative to the ribcage.

turtle

Turtles are known as an all-around zoological mindfuck. Their phylogeny is all over the place, their shell is unique, as is the position of the shoulder girdle. In this paper, the authors document the shoulder girdle’s position and relation to the ribcage and shell in all major amniote groups. The result is that the turtle condition isn’t the wonky one – it’s actually the basal condition from which the shoulder girdle of the other amniotes evolved. This has numerous implications, on the one hand for our conception of amniote evolution, and on the other hand for the way we study turtles. Nowadays, we compare the development of the turtle with development in chickens and mice. But, as this paper shows, mice and chickens are completely unsuitable because they’re evolutionarily too derived to be of any use for the question (that’s also a criticism I level to almost all model organism-centered research, but that’s outside the scope here).

More support for this model can be found in some phylogenies that find that lizards and turtles are closely related. These have traditionally been a subset of morphological phylogenies, but now a molecular one, MicroRNAs support a turtle + lizard clade, has been published too.

5. The oyster genome reveals stress adaptation and complexity of shell formation. [OA]

oysterdefence

Oysters may look peaceful, but their lives are very stressful. They live in an environment where their shell is the only defence against predators, and where they are subjected to drastic environmental changes when at low tide. A lot of their coping mechanisms are epigenetically-mediated, e.g. the number of size of spines on spiny oysters are a function of how many predators are around, but there is a lot of underlying genomic machinery enabling those. This paper presents a draft genome of the oyster Crassostrea gigas and finds that they have a lot of unique genes related to stress tolerance (see diagram above) and controlling the formation of the shell. I’d be interested in comparing with other oysters that may not live in intertidal habitats.

4. Metazoan opsin evolution reveals a simple route to animal vision.

opsin

Whatever challenges once existed to explain the evolution of vision have all crumbled away. While I find the popular explanation a bit lacking and simplistic for my tastes, the full version of the morphological explanation is clear. This paper takes care of the molecular side by showing that opsins, one of the main photopigment classes, evolved as parsimonioulsy as one could imagine: it can all be explained with just two duplications in the neuralian stem, and one earlier on, as shown in the diagram above.

But why limit ourselves to opsins? Vision is even found in the sponges, those nerve-less animals. As Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin shows, the sponge larva can follow light and uses a cryptochrome pigment in a ring structure to do so. This ring structure thus counts as an eye.

Speaking of eyes, A Unique Advantage for Giant Eyes in Giant Squid tells us why giant squid have giant eyes: to detect predators more than 100 meters away, even in the deep sea.

3. The First Record of a Trans-Oceanic Sister-Group Relationship between Obligate Vertebrate Troglobites. [OA]

gobies

The awesome result fo this paper is based on a new molecular phylogeny of the gobies. The result is shown in the diagram above: the genera Typhleotris and Milyeringa are sisters, I.e.t hey descend from the same common ancestor. Both of thes egenera are troglobitic, living in caves. But here’s the spectacular thing: one genus is endemic to Australia, the other to Madagascar. That these two are sister means that they split from each other back when eastern Gondwana broke up in the mid-Cretaceous, so this is a case of long-term vicariance. Although there is the alternate possibility that the split happened afterwards in the proto-Indian Ocean, either case is a testament to the importance of integrating (palaeo)geography into evolutionary studies.

2. Evolution of a Novel Muscle Design in Sea Urchins (Echinodermata: Echinoidea). [OA]

frilledmuscle

The picture above shows the position and details of a type of muscle found in some sea urchins, called frilled protractor muscle. It’s a strange type of muscle found interacting with Aristotle’s Lantern (the “teeth” of a sea urchin), and this study looks at its taxonomic distribution in detail using MRI. The main difference between these muscles and the others are that these ones have frills, which in turn allows more muscle fibers to reach a greater area – it’s basically increasing the surface area to volume ratio. There is no certain function for them yet: the authors found no correlation except that the species that have them also have keeled teeth, so it may be related to feeding; otherwise, the surface area:volume ratio increase could provide a metabolic advantage. However, without a robust phylogenetic tree for the sea urchins (doesn’t exist yet), nothing can be said for sure yet, although the authors tentatively say it’s a monophyletic feature (I’d say it’s the opposite, but a phylogenetic tree is needed to confirm anything!). In any case, any new type of muscle is a cool finding, which is why this gets a top spot. Another reason is for demonstrating that methodological advances always happen in zoology (nowadays, use of such advanced imaging techniques), so we zoologists do need funding.

Independent evolution of striated muscles in cnidarians and bilaterians is somewhat related in that it also deals with new muscle types, finding that the genetic core underlying striated muscles are already present way back in the unicellular protozoans, and are even expressed in sponges. Analysis of the genetic repertoire and expressions of these necessities for striated muscle then showed that cnidarians and bilaterians evolved them convergently, with cnidarians missing some key aspects of bilaterian striated muscle, and expressing those genes for purposes other than striated muscle.

1. Neural Correlates of a Magnetic Sense.

That birds can sense the magnetic field has long been known. Recently, experiments have shown that they detect the magnetic field through magnetic pigments in one of their eyes. Now this paper adds more pieces to the puzzle by finding how the information is encoded for transmitting to the brain of the homing pigeon. Basically, there are 53 single neurons in the brainstem that record the direction, intensity, and polarity of the magnetic field.

Another interesting brain- and locomotion-related paper is Specialized brain regions and sensory inputs that control locomotion in leeches, which experimentally finds out which brain regions control which aspects of swimming and crawling in a leech.

Well, that’s it for the “2012 in review” series. Hope you enjoyed it, and you can expect a repeat at the end of this year.

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


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Categories : Evolution, Mollusca, Vertebrates, Vision, Zoology

Top Books of 2012: Zoology

25 12 2012

Jump to another list: Environmental and Climate Change; Evolution; Historical Geology; History of Science; Human Evolution and Anthropology; Palaeontology.

These are books about animals. Some are layman-oriented, others are complete academic texts, so your mileage may vary. And with this post, the Top Books of 2012 comes at an end… but the series continues tomorrow with the real meat: the top discoveries of 2012, outlined in a total of 11 posts.

  1. Cardé & Resh (eds.). A World of Insects: The Harvard University Press Reader. (Harvard University Press)
978-0-674-04619-1-frontcover This is an excellent anthology of some of the groundbreaking studies in entomology. It’s compiled not for the entomologist, but for the layman, so it’s also very accessible. If you’re at all interested in insects, or have children who are into nature, or are a science/biology teacher, this books is perfect for you.
  1. Hughes, Brodeur & Thomas (eds.). Host Manipulation by Parasites. (Oxford University Press)
host-manipulation-by-parasites Who doesn’t think behaviour-manipulating parasites are awesome? No reader of this blog, I can guarantee that based on readership statistics of this post. This book is an authoritative review of the phenomenon, written by leading researchers, with the contributions of behavioural ecologists to help integrate the organismal, neurobiological, and evolutionary aspects with behavioural and ecological aspects of this sort of parasitism. It’s academically-oriented, but if you can get through my posts, you should have no problems reading the book. And I really do recommend it, because the subject matter is absolutely lovely.
  1. Brunetta & Craig. Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating. (Yale University Press)
spider-silk-evolution-and-400-million-years-of-spinning-waiting-snagging-and-mating A 2012 paperback release of a 2010 hardback, this book is worth re-advertising because it’s really great. If you’ve ever wondered about the diversity of silk in spiders, the myriad different uses of silk in spiders, and just how silk use has evolved to fulfil all these uses, then this book is exactly what you need. Highly recommended for any arachnophiliac of any level.
  1. Gould & Gould. Animal Architects: Building and the Evolution of Intelligence. (Basic Books)
animal-architects-building-and-the-evolution-of-intelligence One of my favourite pet topics is animal intelligence (e.g.). If you’re also interested in it, then you should look into getting this book. It’s a compendium of architecture produced from all over the animal kingdom, examined in the light of behavioural biology and intelligence.
  1. Land & Nilsson. Animal Eyes. (2d ed.; Oxford University Press)
animal-eyes An excellent resource for anyone interested in anatomy and sensory physiology. All types of animal eyes are  detailed in this book, along with their efficiency and nervous integration (how they’re used to make images), and evolutionary histories. It’s written by two leading authorities on the subject, so if you want a comprehensive overview of animal vision, this is it.
  1. Fortey. Horseshoe Crabs and Velvet Worms: The Story of the Animals and Plants That Time Has Left Behind. (Knopf)
horseshoe-crabs-and-velvet-worms-the-story-of-the-animals-and-plants-that-time-has-left-behind This book is a natural history of various “living fossils” – not to worry, the fallacies of the term “living fossil” are explained in the book. Written by Richard Fortey, a veteran invertebrate palaeontologist who’s written a lot of other popular science books, all of which rank among my favourites. I could quibble that this one is a bit low on science compared to his other books, but it’s still a wonderful read.
  1. Sagarin. Learning From the Octopus: How Secrets from Nature Can Help Us Fight Terrorist Attacks, Natural Disasters, and Disease. (Basic Books)
sagarain-learning-from725e Whenever people ask me what the point to being a zoologist is, or what the purpose of my research is, I struggle for an answer – I’m one of those hedonistic scientists, doing science just for the sake of satisfying my curiosity and thirst for knowledge. After reading this book, I don’t have to make stuff up anymore. Sagarin goes through various adaptations that organisms have, and uses them as inspiration for suggestions on how to improve our own ways of doign things in politics, security, and much more. It’s a light-hearted book, not an academic one, so I fully recommend it for an easy and fun read.
  1. Waldbauer. How Not to Be Eaten: The Insects Fight Back. (University of California Press)
how-not-to-be-eaten-the-insects-fight-back From hiding to playing dead to spitting acid to blowing themselves up, insects have many ways to defend themselves – and their predators have coevolved to dispatch those defences. This book is all about this fascinating stuff, and is aimed at the lay public, so get it if you want interesting tales and factoids from the world of insect natural history.
  1. Weis. Walking Sideways: The Remarkable World of Crabs. (Cornell University Press)
80140100864250L I know for a fact, from eating together with lesser beings who have not studied invertebrate zoology, that there is a huge demand for general books about invertebrate groups, similar to the myriad ones we have for charming vertebrates. This one covers it for crabs. Aimed at the lay reader, it goes through all the basics of crab biology and ecology. Reading it is like having a seafood lunch/dinner with me. It’s also suitable for more advanced readers, since it has a good literature list.
  1. Krasnov. Functional and Evolutionary Ecology of Fleas: A Model for Ecological Parasitology. (Cambridge University Press)
functional-and-evolutionary-ecology-of-fleas-a-model-for-ecological-parasitology A 2008 hardback re-published in 2012 as a paperback. My list, my rules: this counts as a new book. It’s all about fleas, but using them as a case study for the evolutionary and ecological aspects of parasitology. So it’s really of interest to anyone whos tudies parasitology. It’s an academic textbook though, not quite easy reading for a non-biologist.

Jump to another list: Environmental and Climate Change; Evolution; Historical Geology; History of Science; Human Evolution and Anthropology; Palaeontology.


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Categories : Crustacea, Entomology, Spiders, Zoology

Flatfish (Vertebrata: Pleuronectiformes)

9 08 2012

Pleuronectiformes (flatfish) is an order composed of almost 800 species in 11 families (Eschemeyer & Fong, 2011), distributed cosmopolitanly in mostly marine waters, although some can also be found in freshwater. They’re most well-known from the edible flounders, turbots, halibuts, and soles, all of which have well-established aquaculture schemes. For example, 9067 tons of turbot were produced in Europe in 2008, a number that pales in comparison to the 60000 tons produced in China.

They have a very derived morphology as is made clear from the above picture (Lee et al., 2009), and a correspondingly small genome that’s half the size of other fish. Flatfish are a classic example of asymmetry in a taxon that is characterised by symmetry, the Bilateria. The larva is a bilaterally symmetric, free-swimming larva. On metamorphosis to the benthic adult, the body can be skewed to the left or to the right: they become flattened, undergoing a series of drastic changes whereby one side stays facing the bottom, while the other (including the eyes) faces the water.

Below is a Youtube video of the inimitable David Attenborough explaining the development of flatfish.

The eyes-on-one-side-of-the-adult-head is considered to be an autapomorphic feature for the Pleuronectiformes (Friedman, 2008). It should be noted that some molecular analyses don’t recover the Pleuronectiformes as a monophyletic grouping (Smith & Wheeler, 2006), but this is most probably due to the shortfalls of molecular phylogenetics.

As Palmer (1996) points out, the side to which the basalmost flatfish are skewed isn’t genetically set, but is determined environmentally. Only in more derived flatfish has one side been developmentally favoured over the other, e.g. Cynoglossidae (tonguefish) are always left-skewed.

Other changes associated with the benthic lifestyle include the loss of the swim bladder – they don’t need to float around, after all.

They have basic camouflaging abilities, being able to mix up to three patterns to camouflage their body according to their current location (Kelman et al., 2006). I don’t imagine they need the more complex camouflaging abilities found in cephalopods (where the chromatophores allow an almost unlimited arrangement of patterns), given that they only live on the benthos (sometimes for over 20 years, which is a pretty impressive lifespan). The way the colour-changing works is by having special pigment-containing organelles in the chromatophores that are pushed around in the cell by the cytoskeleton to form the different colours.

References:

Eschemeyer WN & Fong JD. 2011.Pisces. In: Zhang Z-Q. (ed). Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness.

Kelman EJ, Tiptus P & Osorio D. 2006. Juvenile plaice (Pleuronectes platessa) produce camouflage by flexibly combining two separate patterns. JEB 209, 3288-3292.

Friedman M. 2008. The evolutionary origin of flatfish asymmetry. Nature 454, 209-212.

Lee M-Y, Munroe TA & Chen H-M. 2009. A new species of tonguefish (Pleuronectiformes: Cynoglossidae) from Taiwanese waters. Zootaxa 2203, 49-58.

Palmer AR. 1996. From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance. PNAS 93, 14279-14286.

Smith WL & Wheeler WC. 2006. Venom Evolution Widespread in Fishes: A Phylogenetic Road Map for the Bioprospecting of Piscine Venoms. Journal of Heredity 97, 206-217.


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Elysia and Other Photosynthetic Sea Slugs

16 06 2012

Elysia is an “opisthobranch” sea slug famous on the internet for its remarkable ability to photosynthesise, giving it the nickname of “solar-powered sea slug”. It does this by kleptoplasty – stealing plastids from its algal food. If you note the greenish colour in E. asbecki above (Wägele et al., 2010), the green comes from the harvested chloroplasts. This post will look at this process, and generally at the biology of the genus.

Before starting, it’s worth noting that while Elysia is the most famous of these examples on the internet, it’s definitely not the only animal that can photosynthesise by symbiosis with algae. Falkowski & Knoll (2007) have a three page-long table (pp. 90-92) listing various eukaryotes where this has been documented, including sponges, corals, ascidians, flatworms, and bivalves.

E. chlorotica, if internet fame is anything to go by, is probably the poster child for the phenomenon, and also the one that exhibits it the best. It can harvest the chloroplasts from any number of ulvophycean and xanthophyte algae, but the most successful relationship is with the xanthophyte alga, Vaucheria litorea. The chloroplasts get sequestered intracellularly in the digestive epithelium, and stay functional for over 14 months (Rumpho et al., 2006). This isn’t just an opportunistic relationship, but one that has evolved into a real symbiosis, as evidenced by the identification of lateral transfer of V. litorea nuclear genes into the E. chlorotica genome (Schwartz et al., 2010), most tellingly the transfer of the oxygenic photosynthesis gene, psbO, and fcp, associated with light-harvesting complexes (Rumpho et al., 2008). This is also the reason why naming it a symbiosis may be a mistake, as it doesn’t involve two genetically independent organisms (Law & Lewis, 1983). Nomenclature aside, the chloroplast is hugely beneficial for the slug, as it provides “free” carbohydrates at times when food isn’t available (e.g. in winter, when host algae don’t grow).

Interestingly, the algal chloroplast loses its host membrane and outer two of the four chloroplast membranes (Rumpho et al., 2000) and is found free-living in the cytoplasm in adults after getting phagocytosed (Rumpho et al., 2000). In juveniles, they are bound within a special membrane.

Elysia contains over 120 species, accounting for ~40% of all sacoglossans. In fact, the phenomenon was first discovered in E. atroviridis, not E. chlorotica (Kawaguti & Yamasu, 1965), with functionality of chloroplasts documented by Taylor (1967) and evidence that the chloroplasts contribute to the animal’s metabolism by Trench et al. (1972). Other Elysia species do not nearly have E. chlorotica‘s efficiency, with most retaining the chloroplast for a couple of months at best, after which the chloroplasts degrade and get enveloped in phagosomes and presumably digested (Marín & Ros, 1993). Feeding allows chloroplasts to get replaced, but this is limited by the presence of algae. It is however notable that chloroplasts from multiple species can get sequestered (Curtis et al., 2006), so it’s not necessarily a specific interaction.

Elysia belongs to the Plakobranchidae, a family where long-term plastid retention is autapomorphic (Händeler et al., 2009) and lasts over a couple of weeks generally, but outside of the family, the association lasts for no more than a week. Individuals behaviourally try to control light intensity in order to maximise the lifespan of the inherited chloroplasts and to regulate photosynthesis rate (Casalduero & Muniain, 2008), but at some point, the chloroplasts just stop working.

A very valid question to ask is how such an association can arise. The ability to acquire plastids from food is most probably an ancestral one in sacoglossans, and is linked to one of the main autapomorphies of the Sacoglossa, a radula with only one row of teeth and one median tooth (Mikkelsen, 1996; pictured above from E. asbecki from Wägele et al. (2010)), which is what allows the animal to pierce the algal cell and suck out the plastids (Jensen, 1997). This is a feeding style that is highly-specialised and not found anywhere else in the molluscs, and underlies the reason why sacoglossans feed only on septate and siphonous algae, with only some also feeding additionally on other plants such as seagrass (Jensen, 1981). Each species, depending on their specificity, can also have further modifications to fit the radula perfectly to its host plant (Jensen, 1994), and it’s likely that host shifts can play a role in diversification and speciation, as hinted at by Trowbridge & Todd (2001)‘s work on the shifting of a Scottish subpopulation of E. viridis to feeding on an invasive alga within the past 50 years.

The retention of plastids can be imagined as having considerable fitness benefits, for example a free food source in the winter when algae don’t grow, or conferring a defensive adantage as camouflage – once they ingest the chloroplasts, the slugs turn green, identical to the background, and this is a tremendous advantage considering their lack of shell. There is also some evidence that their food gives them defensive compounds to sequester as well as chloroplasts, for example chlorodesmin, a fish repellent (Hay et al., 1989).

On to Elysia‘s general biology. The monophyly of the genus is not known for sure, and is strongly supported only by molecular phylogenies (Händeler et al., 2009). Truly diagnostic macroscopic features are not to be found, as is clear from field guides, where sacoglossans are all lumped together as unidentified morphospecies. So if you happen to catch one (your best bet is to look carefully in algal meadows, at any depth, keeping in mind that they will be well-camouflaged), your best bet is to consult an expert or trawl through seaslugforum.net.

As all gastropods, Elysia mating involves “love darts”. Schmitt et al. (2007) describe the process in E. timida, where it basically amounts to a synchronised shooting of hypodermic love darts, followed by a short period of standard vaginal impregnation aided by glandular fluids. You can view3 videos from that paper here. Elysia‘s life cycle involves a planktonic larval stage, with the veliger larva having a sinistral shell and dispersing for a couple of weeks or more. The metamorphosis to the adult takes place when the veliger attaches itself to a film of microorganisms growing in an alga-rich habitat.

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References:

Casalduero FG & Muniain C. 2008. The role of kleptoplasts in the survival rates of Elysia timida (Risso, 1818): (Sacoglossa: Opisthobranchia) during periods of food shortage. Journal of Experimental Marine Biology and Ecology 357, 181-187.

Curtis NE, Massey SE & Pierce SK. 2006. The symbiotic chloroplasts in the sacoglossan Elysia clarki are from several algal species. Invertebrate Biology 125, 336-345.

Falkowski PG & Knoll AH. 2007. Evolution of primary producers in the sea.

Green BJ, Li W-J, Manhart JR, Fox TC, Summer EJ, Kennedy RA, Pierce SK & Rumpho ME. 2000. Mollusc-Algal Chloroplast Endosymbiosis. Photosynthesis, Thylakoid Protein Maintenance, and Chloroplast Gene Expression Continue for Many Months in the Absence of the Algal Nucleus. Plant Physiology 124, 331-342.

Händeler K, Grzymbowski YP, Krug PJ & Wägele H. 2009. Functional chloroplasts in metazoan cells – a unique evolutionary strategy in animal life. Frontiers in Zoology 6, 28.

Hay ME, Pawlik JR, Duffy JE & Fenical W. 1989. Seaweed-herbivore-predator interactions: host-plant specialization reduces predation on small herbivores. Oecologia 81, 418-427.

Jensen KR. 1981. OBSERVATIONS ON FEEDING METHODS IN SOME FLORIDA ASCOGLOSSANS. Journal of Molluscan Studies 47, 190-199.

Jensen KR. 1993. Morphological adaptations and plasticity of radular teeth of the Sacoglossa (= Ascoglossa) (Mollusca: Opisthobranchia) in relation to their food plants. Biological Journal of the Linnean Society 48, 135-155.

Jensen K. 1997. Evolution of the Sacoglossa (Mollusca, Opisthobranchia) and the ecological associations with their food plants. Evolutionary Ecology 11, 301-335.

Kawaguti S & Yamasu T. 1965. Electron microscopy on the symbiosis between an elysioid gastropod and chloroplasts of a green alga. Biological Journal of Okayama University 11, 57-65.

Law R & Lewis DH. 1983. Biotic environments and the maintenance of sex–some evidence from mutualistic symbioses. Biological Journal of the Linnean Society 20, 249-276.

Marín A & Ros J. 1993. ULTRASTRUCTURAL AND ECOLOGICAL ASPECTS OF THE DEVELOPMENT OF CHLOROPLAST RETENTION IN THE SACOGLOSSAN GASTROPOD ELYSIA TIMIDA. Journal of Molluscan Studies 59, 95-104.

Mikkelsen PM. 1996. The evolutionary relationships of Cephalaspidea s.l. (Gastropoda: Opisthobranchia): a phylogenetic analysis. Malacologia 37, 375-442.

Rumpho ME, Summer EJ & Manhart JR. 2000. Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis. Plant Physiology 123, 29-38.

Rumpho ME, Dastoor FP, Manhart JR & Lee J. 2006. The Kleptoplast. Advances in Photosynthesis and Respiration 23, 451-473.

Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Chattacharya D, Moustafa A & Manhart JR. 2008. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. PNAS 105, 17867-17871.

Schmitt V, Anthes N & Michiels NK. 2007. Mating behaviour in the sea slug Elysia timida (Opisthobranchia, Sacoglossa): hypodermic injection, sperm transfer and balanced reciprocity. Frontiers in Zoology 4, 17.

Schwartz JA, Curtis NE & Pierce SK. 2010. Using Algal Transcriptome Sequences to Identify Transferred Genes in the Sea Slug, Elysia chlorotica. Evolutionary Biology 37, 29-37.

Taylor DL. 1967. THE OCCURRENCE AND SIGNIFICANCE OF ENDOSYMBIOTIC CHLOROPLASTS IN THE DIGESTIVE GLANDS OF HERBIVOROUS OPISTHOBRANCHS. Journal of Phycology 3, 234-235.

Trench RK, Trench ME & Muscatine L. 1972. Symbiotic Chloroplasts; Their Photosynthetic Products and Contribution to Mucus Synthesis in Two Marine Slugs. Biological Bulletin 142, 335-349.

Trowbridge CD & Todd CD. 2001. HOST-PLANT CHANGE IN MARINE SPECIALIST HERBIVORES: ASCOGLOSSAN SEA SLUGS ON INTRODUCED MACROALGAE. Ecological Monographs 71, 219-243.

Wägele H, Stemmer K, Burghardt I & Händeler K. 2010. Two new sacoglossan sea slug species (Opisthobranchia, Gastropoda): Ercolania annelyleorum sp. nov. (Limapontioidea) and Elysia asbecki sp. nov. (Plakobranchoidea), with notes on anatomy, histology and biology. Zootaxa 2676, 1-28.

Research Blogging necessities :)

Katharina Händeler1, Yvonne P Grzymbowski, Patrick J Krug, & Heike Wägele (2009). Functional chloroplasts in metazoan cells – a unique evolutionary strategy in animal life Frontiers in Zoology DOI: 10.1186/1742-9994-6-28
Mary E. Rumpho, Elizabeth J. Summer, & James R. Manhart (2000). Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis Plant Physiology DOI: 10.1104/pp.123.1.29
Mary E. Rumpho, Farahad P. Dastoor, James R. Manhart, & Jungho Lee (2006). The Kleptoplast Advances in Photosynthesis and Respiration DOI: 10.1007/978-1-4020-4061-0_23


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Xenoturbellida

25 04 2012

Xenoturbellida is the name of a monogeneric phylum erected to accommodate Xenoturbella bocki and X. westbladi; pictured above is X. bocki (Telford, 2008). It’s of special interest for animal phylogeny because of its uncertain position among the basal bilaterians, if not within the deuterostomes. This post is an introduction to the organism and its phylogenetic placement.

First off, it’s necessary to establish that Xenoturbella is indeed a unique animal deserving of its own phylum. Ax (1995) lists four autapomorphies:

  • Epidermal cillia with two parallel roots.
  • Cilliated epidermal cells with support fibril made from bundles of filaments.
  • Subepidermal membrane complex comprising an outer and inner basal lamina and striped filaments in the center.
  • Intraepidermal statocyst with freely-moveable monocilliary cells floating inside it.

Xenoturbella is a wormy marine animal, inhabiting soft substrates up to 100 m deep. It’s white, up to 3 cm long, with conical extremities and a slightly-flattened body covered in cillia (except for an area in the middle of the body). Its epidermis is unusually thick, hence the need for the support fibrils.

The figures above show the anatomy of Xenoturbella, from Telford (2008). The abbreviations below refer to them.

A mouth (m) is found near the middle of the animal, leading directly into the stomach (gc). There is no pharynx and no anus.

Its nervous system is a simple basiepithelial nerve net (np), with no sign of a brain or any true nerve cords. The statocyst (st) at the anterior end of the animal has a nervous plexus associated with it, but that is the only form of nervous system centralisation found. The statocyst itself is enclosed in a capsule, the interior of which contains many monocilliary cells floating around.

Two muscular system are found. The main one is formed by the autapomorphic subepidermal membrane complex running across the entire body (musc), where the filaments are differentiated into longitudinal and circular muscles (lm, cm), allowing peristaltic movement. A second system is found around the stomach (rm).

Their reproduction is very simple. They’re hermaphrodites with no gonads, genital openings or copulation rituals. Eggs and sperm originate in the parenchyma surrounding the intestine (int). Eggs break into the stomach and are transferred to the mouth and released (Beklemishev, 1969); the same is presumed to happen to sperm, although this hasn’t been observed.

When Xenoturbella bocki was first described by Westblad (1949), he placed it as a turbellarian platyhelminth, a hypothesis that has fallen out of favour. Support can be found for them being related to acoelomorphs (Telford, 2008). Shared characters that are potentially apomorphic for such a clade include a ventral mouth, hermaphroditism (plesiomorphic), lack of coeloms, and the arrangement of the nervous system (see Westblad, 1949). The problem is that all of these can easily evolve convergently; more detailed characters involving the structure of the cillia don’t stand up to scrutiny. This relationship, if true, would be very important, since acoels are purported to be pretty basal in bilaterian phylogeny (Ruiz-Trillo et al., 1999) and thus critical to understanding the evolution of animals.

However, what phylogenomics shows us nowadays is that the Acoelomorpha and Xenoturbellida are sisters in the deuterostomes (Philippe et al., 2011), echoing earlier results based on ESTs from the same group of (excellent) researchers (Philippe et al., 2007). The clade is referred to as the Xenacoelomorpha. This is significantly different from having them at the base of the Bilateria, with the main implication being that the evolution of the deuterostomes is one that involves plenty of character losses causing extreme morphological disparity – think of how profoundly different echinoderms, hemichordates, chordates, tunicates, acoels and Xenoturbella are.

The current consensus view, based mostly on nuclear genes, is that Xenoturbella belongs somewhere in the Deuterostomia (Bourlat et al., 2003), most probably as the sister group to the Ambulacraria (as seen in the diagram above, from Telford & Littlewood (2009); see Bourlat et al. (2006)). Mitochondrial genes support them as basal deuterostomes (Perseke et al., 2007). Whether the acoels end up joining them there is still up for more analysis and debate, but given how impressive modern phylogenomic results have been, I personally support it.

An interesting alternative, again from phylogenomics, is that Xenoturbella is itself an acoelomorph (Hejnol et al., 2009). In that study, the Acoelomorpha were recovered as basal bilaterians.

So, to summarise the views for the position of xenoturbellids proposed so far:

  1. Turbellarian flatworms, based on morphology, by Westblad (1949). Disregarded hypothesis.
  2. Sister to Acoelomorpha near the base of the Bilateria, based on molecular evidence.
  3. In the Acoelomorpha near the base of the Bilateria, based on phylogenomics, Hejnol et al. (2009).
  4. Basal Deuterostomia, based on mitochondrial data, Perseke et al. (2007).
  5. Sister to the Ambulacraria (Hemichordata + Echinodermata), based on molecular data, Bourlat et al. (2006).
  6. Clading with the Acoelomorpha as sister to the Ambulacraria, based on phylogenomics, Philippe et al. (2011).

To me, this entire debate revolves around methodology. Simple sequence data, mitochondrial or nuclear, don’t support a close relationship with acoels; phylogenomics does (either as a sister group or as a parent taxon). The way to resolve such a conflict isn’t by simply running more analyses with more taxa or sequences, but to try and understand why this discrepancy exists. For example, we know that molecular evolution rates in acoels and xenoturbellids are rather wonky. How does this affect the analysis? Are there any biases in molecular evolution in the relevant clades (any codon positions or amino acid more prone to change)? These are the questions that have to be asked before wasting more computing power. Once we have the answers, we can build better tools to incorporate the knowledge. Of course, this work is already happening, this isn’t an original thought.

References:

Ax P. 1995. Das System der Metazoa I.

Beklemishev WN. 1969. Principles of Comparative Anatomy of Invertebrates: Organology.

Bourlat SJ, Nielsen C, Lockyer AE, Littlewood DTJ & Telford MJ. 2003. Xenoturbella is a deuterostome that eats molluscs. Nature 424, 925-928.

Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thomdyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR & Telford MJ. 2006. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85-88.

Giribet G, Dunn CW, Edgecombe GD & Rouse GW. 2007. A modern look at the Animal Tree of Life. Zootaxa 1668, 61-79.

Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WEG, Seaver E, Wheeler WC, Martindale MQ, Giribet G & Dunn CW. 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B 276, 4261-4270.

Perseke M, Hankeln T, Weich B, Fritzsch G, Stadler PF, Israelsson O, Bernhard D & Schlegel M. 2007. The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory in Bioscience 126, 35-42.

Philippe H, Brinkmann H, Martínez P, Riutort M & Baguñà J. 2007. Acoel flatworms are not Platyhelminthes: evidence from phylogenomics. PLoS ONE 2, e717.

Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ & Telford MJ. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470, 255-258.

Telford M. 2008. Xenoturbellida: the fourth deuterostome phylum and the diet of worms. Genesis 46, 580-586.

Rohde K, Watson N & Cannon LRG. 1988. Ultrastructure of epidermal cilia of Pseudactinoposthia sp. (Platyhelminthes, Acoela); implications for the phylogenetic status of the Xenoturbellida and Acoelomorpha. Journal of Submicroscopic Cytology 20, 759-767.

Ruiz-Trillo I, Riutort M, Littlewood DT, Herniou EA & Baguna J. 1999. Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes. Science 283, 1919-1923.

Telford MJ & Littlewood DTJ. 2009. Animal Evolution: Genomes, Fossils, and Trees.

Westblad E. 1949. Xenoturbella bocki n. g. n. sp., a peculiar, primitive Turbellarian type. Arkiv for Zoologi 1, 11-29.


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