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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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

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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Request Fulfilment: Extinct Neopterygii

15 02 2013

I was requested by an anonymous person who is most likely a first year palaeo student preparing for their very first seminar to give an overview of extinct neopterygians. I honestly don’t know much about fishies, but I hope these keywords help you search further, my young Padawan.

The majority of modern fish are teleosts, a clade that arose in the Jurassic. However, the clade that contains the teleosts, the Neopterygii, originated in the Late Permian and has several other clades within it. The gars (Lepisosteidae) and bowfins (Amiiformes) are still alive today, albeit only represented by a handful of species each.

sangiorgio

Of the extinct forms, the most well-studied are the ~30 known species of Triassic-Cretaceous Semionotidae, characterised by large dorsal and ventral fins, and almost symmetrical tails. They had a jaw that jutted forward, bearing many small, sharp teeth. The one pictured above is Sangiorgioichthys sui from the famous Luoping locality in China; the fossil is described by López-Arbarello et al. (2011).

macrosemiid

Macrosemiidae lived contemporaneous to the Semionotidae, and are characterised by unique bones in their eye socket, although their most visible feature was their high dorsal fin. Pictured above is a possible Agoultichthys chattertoni from south-eastern Morocco (source: Martill et al., 2011).

pycnodont

Also living in the same period were the Pycnodontiformes. They had the same body type as sunfish – flattened laterally with long dorsal and anal fins, best suited for lying in the sediment of still waters. The tiny picture above is the only pycnodont I could find among my papers, sorry; it’s from Cavin et al. (2010).

Similar in appearance are the Dapediidae, but they are otherwise rather enigmatic, although they seem to be closely related to the Semionotidae. They lived in the Jurassic and Triassic. I have no papers on them and no pictures of them, only these scribbled sentences from lecture notes. Sorry.

I recommend Benton’s Vertebrate Palaeontology, it should have more info on all of these, or at least references to books or reviews specifically on fish evolution.


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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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Top Research of 2012: Human Evolution

5 01 2013

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

My top 10 picks for research dealing broadly with human evolution, which I categorise broadly from primates all the way to cultural evolution in Homo sapiens. I only call it “human evolution” because that gets people’s attention. The master list contains 29 papers. [OA] indicates open access papers.

10. Evolutionary Development in Australopithecus africanus.

This paper studies ontogeny – development from child to adult – in Australopithecus africanus (the Taung child). McNulty finds that the species exhibits paedomorphism: the adult resembles the juvenile of the ancestral species. Specifically in this case, the adult resembles juvenile chimps, because the growth rate decreases after the first molar erupts – a fairly early time. The significance here is that it just provides more data points for the role of paedmorphosis and other forms of heterochrony (messing around with the timing of development) in the evolution of hominins.

9. Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. [OA]

One of the most significant findings of the Neanderthal genome sequencing project was that there was Neanderthal DNA in humans, explainable only by saying that humans and Neanderthals interbred (specifically, in the Middle East, before the consequent spreading into Eurasia). The significance, as far as I’m concerned, is only for species concepts in hominins (how can Neanderthals be a separate species if interbreeding was possible?), but it also allows for many interesting questions: how do we explain the presence of 1-4% Neanderthal DNA in non-African humans? Why isn’t there more? How frequent and common was the interbreeding? This paper attempts to answer these with a probabilistic population genetics model in which humans and Neanderthals are equally fit and coexisting (if that assumption bothers you, it actually squares up with recent research into Neanderthal biology, so it’s warranted). The result is that successful interbreeding was quite rare: 1 pair every 77 generation is enough, although more are allowed by the model with slightly less probability. The rarity of the events is either due to biological reasons (sterile hybrids) or, more interestingly, due to cultural segregation.

Speaking of Neanderthals and humans, Volcanic ash layers illuminate the resilience of Neanderthals and early modern humans to natural hazards shows that they both weren’t much bothered by natural disasters.

8. Evolutionary morphology, cranial biomechanics and the origins of tarsiers and anthropoids.

tarsier

This is a detailed paper on the tarsier fossil record, and what it says about the evolution of tarsiers and especially their skull. It’s significant to study these because tarsiers are pretty close to the anthropoids (the group of primates that includes great apes and monkeys, i.e. humans as well), either as a sister group or as a final remnant of a larger and now mostly extinct clade. The authors support the latter hypothesis, but do admit that the fossil record is currently too sparse to support either view conclusively. Their most important evidence is in the skulls. Tarsiers, as the drawing above shows, have huge eyeballs – the largest relative eyeball size in all mammals. Associated with this is a highly-specialised skull to support the eyeballs and their knocking about as the tarsier leaps around trees. Fossil tarsiiforms also have a similar skull, therefore modern tarsiers must be nested within that group. Otherwise, they would have had to have evolved convergently, which just isn’t parsimonious. However, it’s also true that the body fossil record of these tarsiiforms doesn’t show that they were leaping animals like modern tarsiers. Read the paper for much more in-depth discussion – it also serves as an excellent review paper, including on the history of research into tarsier origins. It also has interesting things to say about how phylogenetics should work – not by calculation, but by functional and ecological consideration. And that’s a view I sympathise with (I try to incorporate both in my own research).

7. U-Series Dating of Paleolithic Art in 11 Caves in Spain.

art

In this paper, Pike et al. present their absolute dating of cave art Spain. The difference from previous studies is that previous studies have not dated the art itself, but the calcite that covers it, which introduces uncertainties into the dating; this study dates the actual artwork directly. The most significant find is a pushing of the oldest cave art by 4000 years: the prvious record was in Grotte Chauvet, France, at 35-39 ka. The new record is from El Castillo at 40.8 ka. The other significant finding is the confirmation that there is indeed an increase in artistic complexity over time, both visually and spiritually.

Such increasing complexity is emblematic of human culture. In Identification of the Social and Cognitive Processes Underlying Human Cumulative Culture, Dean et al. show how humans differ from chimpanzees and capuchins in their cultural transmission methods, allowing future generations to build on the insights of previous humans. It all has to do with our enhanced social cognition, with the four keywords being: pedagogy, communication, imitation, prosociality.

6. Late Middle Eocene primate from Myanmar and the initial anthropoid colonization of Africa.

afrasia

This paper describes the teeth of a new species, Afrasia djijidae, from the late Middle Eocene of Myanmar. The authors conclude that it’s the sister taxon to the contemporaneous Afrotarsius libycus from Libya. If this isn’t the result of convergence, then this gives us a precise timing for at least one dispersal of stem anthropoids into Africa: an Afrasia population migrated across the Tethys to Africa and radiated. It’s very likely that this was one of many such dispersal events however, so don’t go around treating Afrasia as your n(great)-grandfather – there could well have been other stem anthropoid dispersals, if phylogenies are to be trusted (they are).

5. Insights into hominid evolution from the gorilla genome sequence. [OA]

gorilla

The biggest surprise here is that gorillas are really, really close to humans. I would be interested in seeing a brand new thorough phylogenetic study of African great apes, taking phylogenomics (all African great apes are now sequenced) and morphology into account. In any case, there’s a lot of information in this paper, and it’s open access, so go ahead and read it. The key points to take away are that there is a lot of parallel genetic evolution that took place in gorillas, humans, and chimps; and gorillas split away from chimps and humans 10 million years ago.

4. New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo.

This paper describes two lower jaws and a face discovered in 1.78-1.95 Ma deposits in Kenya. I can’t go into the details of them in any comprehensible way, suffice it to say that they’re only 2 new Homo species.

With the addition of more Homo species on the basis of only morphology, there are always detractors that find the evidence tenuous and would rather have larger, more inclusive species (they’re called lumpers, as opposed to splitters who like many species). In Unexpectedly many extinct hominins, phylogenetic methods are applied to estimate how many extinct species should be expected from the hominin fossil record. 8 is the optimal number, but up to 27 can be accomodated. So, split away.

For an in-depth look at how splitters and lumpers debate, check out The status of Homo heidelbergensis (Schoetensack 1908) [OA], which goes through the arguments proposed for making H. heidelbergensis a new species.

3. The diet of Australopithecus sediba.

Those of you who follow human evolution remember the huge splash Australopithecus sediba made back in 2010, with 5 papers describing it and its surroundings in one issue of Science. Add this paper to those ones: it describes what A. sediba ate, on the basis of dental wear, isotopes, and preserved microfossils on the teeth. They were herbivores, feeding on leaves and fruit, much like chimpanzees.

2. Metopic suture of Taung (Australopithecus africanus) and its implications for hominin brain evolution. [OA]

metopicsuture

Newborn ape skulls have a hole called the anterior fontanelle (F above). In chimps, this hole closes very early (before eruption of the first molars), while in human newborns it happens after (well, in most humans anyway). The closing is done by the fusion of the metopic sutures (M above)in the skull. The paper says is that this delay in the fusion was a key characteristic that allowed humans to expand their brain size, for three possible reasons: the growth of the frontal neocortex required changes in the skull structure and its organisation, leading to the delayed fusion; the hole gives the head some squishiness, allowing the head to fit through the very tight birth canal; the very high growth rate of the brain demands an expansive skull, provided by the fontanelle. However, it’s not a settled issue, because there are still several questions and holes (heh) in the hypothesis. Most importantly, there is no evidence showing that australopiths, the early hominids used in this study as evidence for the hypothesis, even had a tight trip through the birth canal. If it’s roomy, then their fontanelle is pretty much useless and the hypothesis isn’t very solid. The second issue is that we don’t know whether the fontanelle really is that important. Can we give birth naturally to non-fontanelled babies? If we can, again, these adaptive hypotheses aren’t very good. Third of all, the fusion of the metopic suture may not even be “predetermined”, and may in fact just arise naturally through biomechanics (chewing especially puts pressure on the skull and may lead to the fusion in the newborn). Again, the lack of an inheritable pathway puts the adaptive hypotheses on shaky ground.

1. A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations.

foot

The popular narrative of chimp-like ancestors coming down from trees, going out into the savannah and becoming humans is increasingly being shown to be oversimplified to the point of wrongness (and I’ll be damned if creationists quote-mine me there). The foot fossils described here add to the complexity of the story. They’re eight bones from a right foot, from a 3.2 – 3.8 Ma locality in Ethiopia. The graph above shows why the foot is significant: it’s the black star, and clusters neatly with humans and gorillas – the non-tree dwelling apes. Anatomical examination shows that the foot is equally adapted to grasping tree branches and to being walked on – in other words, the species that had it was at least facultatively bipedal. What this means in the larger context of human evolution is that bipedalism isn’t something special – it can, and has, evolved convergently.

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


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Top Books of 2012: Palaeontology

24 12 2012

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

These are my top 10 palaeontology books of the year, running the gamut from historically-oriented books detailing the histories of palaeontological discoveries and of the science of palaeontology to books about now-extinct animals (e.g. dinosaurs). There is one children’s book (about dinosaurs, of course; #10), with most of the books aimed at educated laymen or working biologists; a couple of purely academic books are mixed in too.

  1. Long. The Dawn of the Deed: The Prehistoric Origins of Sex. (University of Chicago Press)
9780226492544_p0_v1_s260x420 I had to debate myself about whether to put this awesome book in the zoology or the palaeontology section, because it is part overview of weird ways animals have sex, and part scientific memoir of Long’s palaeontological research and findings. In the end, the palaeontological stuff wins out, because Long uses his research to illuminate the evolution of sex. In any case, I recommend anyone to read this book just for the quirkiness described in it, and also to see how exceptional finds in palaeontology can give us insights into things we wouldn’t think palaeontology would have a say about.
  1. Falk. The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution. (University of Chicago Press)
full-cover-Falk_Fossil-206x300 A 2012 paperback release of a 2011 hardback, this book is an insider’s account of the scientific and popular controversies of the varying interpretations of the Taung child and of Homo floresiensis. I have a thing for these kinds of books that don’t just talk about the facts, but also give the perspective of the scientist who is working on them, because it gives the best view on how real science evolves and progresses, away from the idealised conceptions of philosophers. This book is an excellent showcase of that, using two prominent fossil cases and described by Falk, whose illustrious career in part revolved around them.
  1. Fastovsky & Weishampel. Dinosaurs: A Concise Natural History. (Cambridge University Press)
dinosaurs-a-concise-natural-history This is the ultimate book for someone who’s not a dinosaur palaeontologist, but is nonetheless interested in the biology and study of dinosaurs. It’s not a textbook, but it’s not some picture guide. It’s a comprehensive overview of what we currently know about dinosaurs, without the niggly anatomical details that a proper textbook like The Dinosauria would have. It also discusses the open questions that we have. In all, a great resource for anyone from the serious amateur to the professor stuck teaching about dinosaurs even though they’re not his/her specialty (it’s happened to me several times).
  1. Sánchez. Embryos in Deep Time: The Rock Record of Biological Development. (University of California Press)
9780520271937 Non-palaeontologists are often surprised at the fact that we have preserved life history stages of various animals – from vertebrates of different ages to the moult stages of trilobites (the majority of trilobite fossils are in fact exoskeletons discarded after moulting). This book exposes them all to show the utility of palaeontology in studying the evolution of development. I was impressed by the phylogenetic breadth it covers, including examples I had no idea about.
  1. Sepkoski. Rereading the Fossil Record: The Growth of Paleobiology as an Evolutionary Discipline. (University of Chicago Press)
rereading-the-fossil-record-the-growth-of-paleobiology-as-an-evolutionary-discipline This book arguably belongs in the history of science list, but I’ll put it here because it’s more relevant to palaeontology as a science. It’s an outline of the history of palaeobiology, the field that combines palaeontology and evolutionary biology, using fossils to study evolution and evolutionary patterns. For a long time, palaeontologists were regarded as irrelevant stamp collectors (it’s a view that still persists among idiotic scientists); palaeobiology turned that over on its head. The book overall is excellent, going from the 19th century to the present; if I had one qualm, it’s what I perceive as a bit of US-centrism, but that may be due to my education in Germany exposing me to palaeontologists who presaged palaeobiology’s development as a field.
  1. Maxwell. Piltdown Man and Other Hoaxes: A book about Lies, Legends, and the Search for the Missing Link. (American Book Publishing)
piltdown-man-other-hoaxes-book-about-lies-legends-jonathan-maxwell-paperback-cover-art A book on scientific hoaxes. It’s not an academic text, just a breeze through some prominent ones, especially those involving palaeontology and cryptozoology. I include it here because of the large section on Piltdown Man.
  1. Berta. Return to the Sea: The Life and Evolutionary Times of Marine Mammals. (University of California Press)
return-to-the-sea-the-life-and-evolutionary-times-of-marine-mammals Arguably a book that should be in the zoology list, I put it here because it discusses the fossil history of cetaceans and pinnipeds and takes a deep time view of everything. Despite its somewhat high price, it’s actually easy-reading and I easily recommend it to the interested layman.
  1. Reynolds & Gallagher. African Genesis: Perspectives on Hominin Evolution. (Cambridge University Press)
african-genesis-perspectives-on-hominin-evolution Please note that there’s a strange screwup with Amazon link above: the title is some weird quantum stuff, but the rest of the page is on this book. This is an academic text containing a comprehensive review of all known hominin fossils and what they tell us about human evolution, as well as current open questions and unknowns. Not easy reading, but if you’re a palaeontologist or palaeoanthropologist looking for the most up-to-date human palaeontology compendium, this is it.
  1. Meredith. Born in Africa: The Quest for the Origins of Human Life. (PublicAffairs)
born-in-africa-the-quest-for-the-origins-of-human-life A 2012 paperback of a 2011 hardback, this is a book bridging history of science with human palaeontology, explaining the history of the major findings in human palaeontology and their implications, and how our views on hominin evolution have evolved in the light of new discoveries. Highly recommended if you’re into human evolution (I’m not, hence the low placing).
  1. Gee & Rey (ill.). A Field Guide to Dinosaurs: The Essential Handbook for Travelers in the Mesozoic. (Chartwell Books)
9780785829027 This is by far the current best dinosaur book for children. It’s got gorgeous illustrations by Luis Rey, one of the top palaeoartists today, it’s as accurate as can be for the intended audience, and the descriptions and information are even usable for middle and high school students. So, in all, if you’re looking for a book to give to a child or teen who’s fascinated by dinosaurs, this is the ultimate one.

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Top Books of 2012: Human Evolution and Anthropology

23 12 2012

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These are books about human evolution, anthropology, and related subjects. Most are in the “educated layman” or undergrad category, with some layman and some complete academic books.

  1. Mitani, Call, Kappeler, Palombit & Silk (eds.). The Evolution of Primate Societies. (University of Chicago Press)
9780226531724 No general discussion of human “nature” and sociology is valid without reference to our evolutionary ancestry. If it’s one of your favourite discussion topics, then get this book so you don’t make elementary mistakes. It basically reviews the ecology, behaviour, and sociology of the social primates and thus allows you to make comparisons. It’s also a surprisingly affordable book for its content.
  1. Hetherington. Living in a Dangerous Climate: Climate Change and Human Evolution. (Cambridge University Press)
living-in-a-dangerous-climate-climate-change-and-human-evolution My most basic summary quip of human evolution goes like this: “Humans are a primate species that got super-lucky with coincidental climate changes allowing them to spread globally.” Because that basically sums it up – our evolution was enabled and pushed first and foremost by climate. That much is clear from any historical geology or human evolution book, and what makes this book great is that it doesn’t look at our evolutioary past, but also to how our self-inflicted climate changes will affect us in the future.
  1. Fuentes. Race, Monogamy, and Other Lies They Told You: Busting Myths about Human Nature. (University of California Press)
race-monogamy-and-other-lies-they-told-you This is a must-read book by everyone. Period. I actually waste a significant amount of time every week trying to drill the stuff told in this book into the heads of ignorant morons who think that there really are living human subspecies who also think that men and women are totally different species, and who think that societally-engendered tropes are actually reflections of biological realities. It’s infuriating, and this book is a one-stop shop for debunking all these idiocies and more. Get it if you buy into them or hang around people who do.
  1. Stringer & Andrews. The Complete World of Human Evolution. (2nd ed.; Thames & Hudson)
the-complete-world-of-human-evolution If you need an affordable, authoritative, up-to-date guide on the ape fossil record (including humans, obviously), this book is exactly what you’re looking for. It’s written specifically for a lay audience – besides the chapters on the fossils, there are introductory chapters introducing palaeontological techniques, so you know how all the information is gathered. It also has a lot of diagrams for easy and effective visual comparisons. All in all, an excellent and comprehensive guide to human evolution that’s accessible to anyone.
  1. Wilson. Consider the Fork: A History of How We Cook and Eat. (Basic Books)
13587130 I classify this book as an anthropological one. It discusses the history of cooking and eating from the discovery of fire to our modern hi-tech kitchens. Some may protest my including it here, but our food has always been one of the important factors in our evolution (from fire to agriculture to the myriad local adaptations, e.g. the teeth of Peruvians, or convergent lactose tolerance in several population; see book 10), so this is a useful book to keep, even if the majority of it focuses on cooking methods rather than the food itself. Plus, it’s pretty interesting!
  1. Stinson, Bogin & O’Rourke (eds.). Human Biology: An Evolutionary and Biocultural Perspective. (2nd ed.; Wiley-Blackwell)
0470179643 This is an academic textbook and is, as far as I can tell, the class of the field when it comes to anthropology: it covers both physical and biological anthropology, and all the links between them. If you’re an anthropology student looking to borrow a book from the library, this is the one you should be looking for (if you’re a student, you probably can’t afford to buy it anyway).
  1. De Duve. Genetics of Original Sin: The Impact of Natural Selection on the Future of Humanity. (Yale University Press)
genetics-of-original-sin-the-impact-of-natural-selection-on-the-future-of-humanity A new paperback release of an older hardback. I don’t care much for the theological blah that occasionally crops up in this book, nor for its ultimate conclusion that we can rise against the power of natural selection, but it is a worthy read because it basically sums up how various social traits that evolution has built into us will basically be our downfall.
  1. Hochberg. Evo-Devo of Child Growth: Treatise on Child Growth and Human Evolution. (Wiley-Blackwell)
170802 One of the critical milestones in human evolution is the addition of a childhood to the life cycle, a period when development occurs very rapidly under the influence of environmental factors. It’s unique to humans, and underlies a lot of our psychology and sociology. This is another academic text, and it has a medical focus, but overall it’s a great book exploring the various stages of childhood and how they relate to our evolution.
  1. Stringer. The Origin of Our Species. (Penguin Books)
The-Origin-of-Our-Species A paperback release of an older hardback. This is the best ultra-basic introduction to human evolution. Get it if you think #4 is too daunting.
  1. Ulijazsek, Mann & Elton. Evolving Human Nutrition: Implications for Public Health. (Cambridge University Press)
evolving-human-nutrition If my blurb to #5 about the importance of food to human evolution intrigued you, then this is the book you’ll want for a comprehensive academic treatment of the subject.

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The Ancestry of Mammals: A Profile of the Synapsida

3 10 2012

Amniotes can be split into two major groups: the Sauropsida and the Synapsida. Synapsids are amniotes with only one large temporal fenestra (the lower one), as seen in the highlighted skull above (Benton, 2004). The sauropsids can have none (anapsid, e.g. turtles) or two (diapsid, e.g. lizards, snakes, dinosaurs). The fourth diagrammed skull with one small temporal fenestra is a euryapsid, and is found only in some extinct marine sauropsids.

Other characteristics of the synapsids include:

  • 1 maxillar canine (or, better said, canine-like tooth), as opposed to a homogeneous bite;
  • Maxillar and quadratojugal bones meet in the cheek;
  • Narrow vertebral arch (where the nerves pass through to the body).

Synapsids split off from the rest of the amniotes during the initial amniote radiation in the swamps of the Carboniferous, with the earliest fossils from the lowest Late Carboniferous (Pennsylvanian, 310 Ma) showing the emergence of the herbivorous Edaphosauridae, one of those famous dinosaurs with the sail on their backs. Readers with an awesome childhood might know these as “pelycosaurs“, but this is a paraphyletic grouping containing the edaphosaurids and several other early “sailed” synapsids, such as the carnivorous Sphenacodontidae (includes the famous Dimetrodon, pictured above from Miller & Harley (2001)) and herbivorous Caseidae, the latter of which were among the largest (3m) tetrapods of their time (Lower Permian) and inhabited dry, upland areas. The sail was composed of the grossly extended spinous processes of the vertebrae and covered by skin, for possible use in thermoregulation, camouflage, or social and sexual communication.

Most “pelycosaurs” went extinct by the Lower Permian after a dominant yet mediocre time on Earth: despite being the very first megaherbivores and megacarnivores, they only managed to spread through western Laurasia (= North America, Europe); by the Late Permian, they had definitively died. One synapsid group subsequently radiated, the therapsids, first known from the Texas Lower Permian Tetraceratops (Amson & Laurin, 2011).

Therapsids quickly rose to prominence and became the dominant organisms until the end-Permian extinction event nearly destroyed them. The three most important groups were:

  • Anomodontia, herbivores and most successful of the ancient therapsids through the diverse and long-lived dicynodonts who had a turtle-like keratinous beak that gave them space for superior mastication abilities and led to their dominance as herbivores;
  • Gorgonopsia, Late Permian carnivores with small eyes and a big and powerful bite; and
  • Cynodontia, the group that includes the mammals.

The aftermath of the end-Permian extinction left only the carnivorous cynodonts and the specialised and dominant herbivorous dicynodonts. The cynodonts radiated in the post-Permian Triassic landscape and by the Late Triassic (225 Ma), the mammaliaforms emerged. These are “mammal-like” insectivores that went on to radiate under the shadow of the dinosaurs in the Jurassic and Cretaceous. They’re called mammal-like because a lot of typically mammalian characteristics are evident in them, especially when it came to cranial and dental features (most important being the dentary-squamosal joint). The KT Event resulted in all but three mammaliaform groups to go extinct. The demise of the non-avian dinosaurs allowed these three groups to radiate and so the modern mammalian fauna was set up, with the monotremes, metatherians (marsupials), and eutherians (placentals) becoming dominant.

I deliberately presented synapsid evolution as a gradual progression towards mammals in this post as summarised in the diagram above (Alberts & Pickler, 2012), despite this being a decidedly bad strategy for teaching the evolution of any taxon. But the evolution of synapsids ending up in mammals is one of the most clear-cut cases of gradual evolution, and this should be stressed. The characteristics known as mammalian characteristics didn’t all pop up in the Tertiary radiation, nor did they suddenly appear in the mammaliaforms, nor in the cynodonts or therapsids.

Instead, they appeared piece by piece, the mammal mosaic becoming gradually more complete at every radiation along the way (Sidor & Hopson, 1998). The most important of these are listed below, in [square brackets] I put in the approximate grade when the changes became noticeable (as far as I’m aware, more knowledgeable readers should correct me!):

  • Changes in skull structure to accommodate larger jaw musculature; included in this is the very important formation of the dentary-squamosal joint, laying the foundation for the ear; [Therapsid]
  • Enlargement of the dentary bone (in the jaw); ["Pelycosaur"]
  • Specialisation of teeth, forming different tooth types; ["Pelycosaur"]
  • Upright stance, as opposed to the crocodile-like sprawl of the other amniotes; [Therapsid]
  • Reduction in ribs to support a diaphragm and thus more active breathing;
  • Secondary hard palate, why we can eat and breathe at the same time; [Therapsid]
  • Respiratory tubinals in the nasal cavity, for accomodating increased metabolic rates by providing an extra pathway for heat release; [Therapsid]
  • Rapid, sustained growth, as opposed to seasonal arresting of growth.

Finally, I want to bring up an enormous pet peeve of mine. You will often hear of synapsids being referred to as “mammal-like reptiles”. This is nonsense, because Reptilia is either defined as synonymous with Sauropsida (with turtles) or with Archosauria (without turtles). Synapsids have nothing to do with reptiles, besides from the fact that they both come from a last common ancestor that was an amniote. Calling them “mammal-like reptiles” is the same as saying that primates are cetaceans. No, they’re not. Cetaceans and primates are their own lines of evolution, and they come from a last common ancestor that was a mammal. Unfortunately, it’s a notation that is traditional and fairly ingrained even in the literature.

References:

Alberts JR & Pickler RH. 2012. Evolution and Development of Dual Ingestion Systems in Mammals: Notes on a New Thesis and Its Clinical Implications. International Journal of Pediatrics 2012.

Amson E & Laurin M. 2011. On the Affinities of Tetraceratops insignis, an Early Permian Synapsid. Acta Palaeontologica Polonica 56, 301-312.

Benton MJ. 2004. Vertebrate Palaeontology.

Miller SA & Harley JB. 2001. Zoology, 5th ed..

Sidor CA & Hopson JA. 1998. Ghost lineages and “mammalness”: assessing the temporal pattern of character acquisition in the Synapsida. Paleobiology 24, 254-273.


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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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