Category Archives: Evolution

Acoelomorpha: A Phylogenetic Headache

ResearchBlogging.orgby Piter Kehoma Boll

Take a look at these guys:

The green worm Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from doris.ffessm.fr

Green worms Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from doris.ffessm.fr

It’s a member of the group Acoelomorpha, animals which are still a puzzle in phylogeny. That means no one knows for sure where in the animals’ evolutionary tree they are exactly.

But first, let’s take a look about what makes an acoelomorph.

Those little guys are small worms, usually measuring less than 1 mm in length and living in marine or brackish waters or as symbionts. There are two groups of acoelomorphs: Acoela and Nemertodermatida. Acoels are the simplest ones; they have a mouth, but lack a gut, so that the food ingested goes directly to the internal tissues. In Nemertodermatida, there is a blind gut, i.e., with only one opening, like in the primitive cnidarians or in flatworms. In fact, they were initially classified as flatworms, but several features later challenged their position inside this phylum. The main differences are:

  • Acoelomorphs have an epidermis (“skin”) with cilia whose roots are interconnected in a hexagonal pattern, while other flatworms have independent cilia.
  • Acoelomorphs lack protonephridia (primitive kidney-like organs) and all other groups of animals have at least one of those or more complex organs with similar function.
  • While flatworms and all other protostomes (arthropods, annelids, mollusks, nematodes…) have ventral nerve cords and deuterostomes (chordates, echinoderms…) have dorsal ones, in acoelomorphs there are several nerve cords distributed radially along the body length.
Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.

Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.

Analyzing such features, it seems obvious that Acoelomorpha is a basal group of bilateral animals and may be the reminiscent of a primitive group of animals later almost completely extinct by their most complex descendants, the true protostomes and deuterostomes. The original radially-distributed nerve cords were simplified in dorsal or ventral ones in higher groups, but remained radial in Acoelomorpha.

Several phylogenetic studies indicate that Acoelomorpha is indeed a basal group of bilateral animals. They also lack several important Hox genes (responsible for determining body plan and organs’ distribution in animals) and it is quite unlikely that they would have lost most of them by secondary simplification.

Another group of simple animals, the Xenoturubellida, was sometimes proposed as a sister group for Acoelomorpha. Their proximity would be explained by several shared features, mainly the simple nervous system, the lack of a stomatogastric (mouth-gut) system, the structure of the epidermal cilia and the unusual fact that, in both groups, epidermal degenerated cells as resorbed in the gastrodermis.

A Xenoturbella worm. Photograph extracted from bioenv.gu.se/english/staff/Hiroaki_Nakano_eng/

A Xenoturbella worm. Photograph extracted from bioenv.gu.se/english/staff/ Hiroaki_Nakano_eng/

The group Xenoturbellida, however, has been placed in Deuterostomia in some molecular studies and recently Philippe et al. 2011 proposed that Acoelomorpha would also belong to the the Deuterostomia! But how could such a thing be possible when they obviously have primitive and unique features, like the radially placed nerve cords? The group’s explanation is that Acoelomorpha, as well as Xenoturbellida, have a sequence of microRNA (miR-103/107/2013) which is exclusive to Deuterostomia, so they would also be deuterostomes.

But wait a minute! What do they mean by “exclusive to Deuterostomia”? It means that that microRNA sequence is found in deuterostomes, but not in protostomes. Now think with me. We have 4 bilateral groups here: Acoelomorpha, Xenoturbellida, Deuterostomiaa and Protostomia. If you look at them this way, we can see that the statement “miR-103/107/2013 is exclusive to Deuterostomia” is false. The truth is that this sequence is absent in Protostomia, but present in all other groups. Wouldn’t it be more logical to think that, instead of deuterostomes acquiring this sequence, what really happened is that it was a primitive microRNA and protostomes have lost it?

If you consider Xenoturbellida and Acoelomorpha inside Deuterostomia, you have to assume that they passed through a huge simplification, and you maintain the radial nerve cords unexplained. Now if you think of them as primitive groups, the only thing necessary is to analyze protostomes as having lost a microRNA sequence. Quite a simpler explanation which doesn’t let open gaps.

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians' ancestor had a complex set of Hox Genes; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians’ ancestor had a complex set of Hox genes, being a complex animal; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.

Position of Xenacoelomorpha as a basal group. It means that (1)

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Boll et al. 2013 (that’s me!) based on a review of previous studies, as a basal group. It means that (1) the bilaterian’s ancestor was a simple animal, with a simple set of Hox genes, having miR-103/107/2013 and radial nerve cords; (2) the set of Hox genes became more complex and the nerve cords where simplified to either dorsal or ventral; (3) miR-103/107/2013 is lost in Protostomia. Way simpler.

You can read more in the references listed below.

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References:

Boll, P., Rossi, I., Amaral, S., Oliveira, S., Müller, E., Lemos, V., & Leal-Zanchet, A. (2013). Platyhelminthes ou apenas semelhantes a Platyhelminthes? Relações filogenéticas dos principais grupos de turbelários. Neotropical Biology and Conservation, 8 (1), 41-52 DOI: 10.4013/nbc.2013.81.06

Egger, B., Steinke, D., Tarui, H., De Mulder, K., Arendt, D., Borgonie, G., Funayama, N., Gschwentner, R., Hartenstein, V., Hobmayer, B., Hooge, M., Hrouda, M., Ishida, S., Kobayashi, C., Kuales, G., Nishimura, O., Pfister, D., Rieger, R., Salvenmoser, W., Smith, J., Technau, U., Tyler, S., Agata, K., Salzburger, W., & Ladurner, P. (2009). To Be or Not to Be a Flatworm: The Acoel Controversy. PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005502

Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G., Edgecombe, G., Martinez, P., Baguna, J., Bailly, X., Jondelius, U., Wiens, M., Muller, W., Seaver, E., Wheeler, W., Martindale, M., Giribet, G., & Dunn, C. (2009). Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society B: Biological Sciences, 276 (1677), 4261-4270 DOI: 10.1098/rspb.2009.0896

Moreno, E., Nadal, M., Baguñà, J., & Martínez, P. (2009). Tracking the origins of the bilaterian
patterning system: insights from the acoel flatworm. Evolution & Development, 11 (5), 574-581 DOI: 10.1111/j.1525-142X.2009.00363.x

Mwinyi, A., Bailly, X., Bourlat, S., Jondelius, U., Littlewood, D., & Podsiadlowski, L. (2010). The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evolutionary Biology, 10 (1) DOI: 10.1186/1471-2148-10-309

Philippe, H., Brinkmann, H., Copley, R., Moroz, L., Nakano, H., Poustka, A., Wallberg, A., Peterson, K., & Telford, M. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470 (7333), 255-258 DOI: 10.1038/nature09676

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Where did milk come from? The mysterious origin of lactation in mammals.

by Piter Kehoma Boll

ResearchBlogging.org In previous posts, I talked about two scientists who introduced “revolutionary” ideas to explain certain aspects in evolution, contradicting what other specialists use to say. But they come up with such unlikely explanations and use to ignore anything that says something contrary to their ideas that no one takes them seriously. You can read about them here and here.

Today, however, I will talk about another scientist who had interesting and innovative ideas, but much more likely and based on many more evidences. His name is Olav T. Oftedal and the topic is the origin of lactation.

As everybody knows, mammals are characterized mainly by the fact that females nourish their young through mammary secretions, the thing we know as “milk”. But how did this trace evolved in the mammalian lineage?

A cat (Nani) with her babies. Photo by Piter Kehoma Boll

A cat (Nani) with her babies. Photo by Piter Kehoma Boll*

Charles Darwin was one of the first ones to think of an explanation. Based on marsupials, Darwin concluded that mammals evolved from animals which carried eggs in a pouch and nourished them by cutaneous secretions. His idea was also inspired by seahorses, were eggs are carried in an abdominal pouch by the male and it was though that they might be nourished by cutaneous secretions too. However the subsequent discovery that the platypus, one the most primitive mammals, lays shelled eggs and have no pouch marked the ruin of Darwin’s theory on the origin of lactation. But… did it indeed?

In a paper published in 2002 in the Journal of Mammary Gland Biology and Neoplasia, Olav T. Oftendal raised some interesting questions and proposed an explanation to the origin of lactation very similar to the one proposed by Darwin one and a half century  before.

As it is known, mammals evolved from a lineage of amniotes called synapsids, from which they are the only extant group, so that everything about their ancestors must be assumed through fossil record.

Mammals’ ancestors are usually called “mammal-like reptiles”, but such a comparison is far away from what they really were. The animals we call reptiles – turtles, snakes, lizards and crocodiles – are sauropsids, so as birds, and they diverged from synapsids soon after the origin of amniotes and were probably very different creatures after some million years.

Let’s start thinking about what’s an amniote. The clade “Amniota” comprises all extant tetrapods other than amphibians, and they are characterized by the presence of a set of membranes surrounding the embryo which assisted in nutrient mobilization, gas exchange and storage of embryonic waste products, as well as in protecting it from the environment in a fluid-filled sac. But how were the eggs of those early amniotes?

When we think of an egg, we use to think of a bird’s egg, with a calcified shell, but this was probably not the case in early amniotes. The eggs of current egg-laying mammals lack a calcareous layer and it is likely that a calcified shell evolved only in the sauropsid lineage.

An ordinary chicken egg is the first think to come to mind for most people when they heard the word "egg". Photo by Sun Ladder, extracted from commons.wikimedia.org

An ordinary chicken egg is the first think to come to mind for most people when they heard the word “egg”. Photo by Sun Ladder*, extracted from commons.wikimedia.org

Eggs without a calcified shell rarely fossilize, and in fact there are no fossil eggs from Carboniferous, Permian and early Triassic, i.e., during all the history of non-mammalian synapsids.

But what’s so good in calcified shells? Well, a calcareous layer helps to prevent water loss from the embryo to the environment, whether to a reduction of relative humidity in the environment or a difference in temperature. Reptiles with non-calcified egg shells use to bury their eggs in damp soil where relative humidity approaches 100%, so dealing with the water loss problem. The increase of aridity from the end of the Permian to the Triassic may have favored the evolution of calcified eggs, but still there is no evidence of synapsid eggs. Could they have buried them in damp soil just as some reptiles do today? It’s possible, but…

Birds and mammals have developed a common feature: endothermy, i.e., “warm blood”. As we all know, birds use that to incubate eggs at elevated temperature, so speeding up the embryo development. It’s quite possible, and likely, that synapsids did the same. But as it was said, the difference in temperature between the egg and the environment also leads to water loss. In birds, the calcified shell solves this problem, but synapsids didn’t seem to have had this advantage.

Observing non-calcified eggs in snakes and lizards, it is possible to notice that they increase in mass by 10 to 100% after being laid. This happens due to water uptake from the environment and, as the shells is not rigid, the egg can also increase in volume, something that cannot happen in rigid-shelled eggs.

According to water uptake, eggs can be classified in endohydric and ectohydric. Endohydric eggs contain all water the embryo needs for the development when it is laid, while ectohydric eggs must take up water from the environment. In non-calcified eggs, it depends mainly of the eggs size. Large eggs may have enough water to sustain the embryo even with some water loss, since their surface:volume ratio is low, but the same cannot be applied to small eggs. And as it is known, the first mammals, and so their direct ancestors, were quite small creatures.

So what we have is an animal with non-calcified egg prone to dehydration and a high body temperature that can help to speed up the embryo development. How to join these two things?

The egg-laying mammal echidna and some marsupials have an abdominal pouch to retain eggs or newborns. It is known that the short-beaked echidnas incubate their eggs in the pouch. Female platypuses don’t have a pouch, but they incubate their eggs by curving their flat tail so that it touches the abdomen, forming a pouch-like enclosure. Inside this pouch, cutaneous secretions from the female’s abdomen would maintain the eggs moist, so preventing dehydration.

An egg of an echidna inside her pouch. (I found this picture on the internet without information about the author and stuff).

An egg of an echidna inside her pouch. (I found this picture on the internet without information about the author and stuff).

A problem in retaining eggs in a pouch is that it constrains the mobility of the parent. To solve this problem, eggs could stay some time inside the pouch to get hydrated and then be removed until it were necessary to rehydrate. This could let the female free from carrying the eggs along all the time and also increase the clutch size beyond the number of eggs that can fit in the pouch. This situation would have favored those females with more cutaneous secretions.

Once the young hatch from the eggs, they could also use the secretion as a source of food, which would lead to a progressive increase in the secretion’s nutritious value until it reached the status of milk.

It makes sense, doesn’t it? It does not contradict any kind of evidence about mammalian evolution and is based on true evidence through fossils and comparison with many kinds of extant groups.

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References:

Oftedal, O. T. 2002. The origin of lactation as a water source for parchment-shelled eggs. Journal of mammary gland biology and neoplasia, 7 (3), 253-66 PMID: 12751890

Oftedal, O. T. 2002. The mammary gland and its origin during synapsid evolution. Journal of mammary gland biology and neoplasia, 7 (3), 225-52 PMID: 12751889

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Does Retallack suffer from Williamson’s syndrome? The land-dwelling Ediacara controversy

by Piter Kehoma Boll

ResearchBlogging.orgAs you may have heard, or read, a paper published this month in Nature claims that the famous Ediacaran biota, a set of fossils from the Ediacaran Period (ca. 635-542 Mya) of the Neoproterozoic Era, is not composed by marine creatures, but rather land lichens. Who made this claim? Gregory Retallack, a geologist at the University of Oregon.

Retallack works on this hypothesis since the 1990s and the main evidences presented by him are related to geological features, like the red color of the rock, which according to him would have a terrestrial origin. Another claim is that if those creatures were soft-bodied animals, they wouldn’t have been so well preserved without compaction, as some fossils have tridimensional features.

Well, I am not a geologist and have no knowledge enough to argue about the geological point of view, neither am I an expert in the Ediacaran biota, but as a biologist I think I can share some thoughts.

First, as it seems, Retallack’s ideas are not accepted by most paleontologists. At the beginning, the innovative view of Ediacaran biota as land-dwelling was interesting, but the arguments to support it are not enough and there are still simpler and more possible explanations for the unusual features of the Ediacaran rocks. This didn’t stop Retallack to pursue in his idea, however, and other paleontologists are getting tired to go on reviewing his papers.

Does such a behavior look familiar? It kind of reminds me of Williamson, whom I talked about some time ago, as you can read here.

Just as Williamson insists in his hybridogenesis idea despite all facts pointing to other directions, so Retallack insists in his land-dwelling lichens hypothesis.

Dickinsonia would have been a land-dwelling lichen, according to Retallack. Photo by Wikipedia user Verisimilus. Extracted from en.wikipedia.org

Dickinsonia would have been a land-dwelling lichen, according to Retallack. Photo by Wikipedia user Verisimilus. Extracted from en.wikipedia.org

Retallack claims that fossils like Dickinsonia and Charnia, despite their bilaterally symmetrical body plan, were lichens. Does anybody know so well symmetrical lichens? And to support this hypothesis, he simply throws any kind of “fungian” explanation for all the fossils, considering the more radially symmetrical ones as bacterial colonies and the more animal-like as simply fungal fruiting bodies. And to explain things like the trace fossils, he talks about land slugs (land slugs during the Proterozoic? Really?) or slime moulds.

But then one might think: does he have any reference to support his ideas? And the answer is: of course, his OWN previous works. There are no other paleontologists claiming the same but himself. It looks just like a case of what I call Williamson’s syndrome.

I’m sure we will find some people supporting his idea, most probably laymen, and they will most certainly use the classical argument “all great scientific discoveries started by being rejected by most of the scientific community”. And I will say that again: Yes, many theories were initially rejected and later proven right, but you cannot forget that many more theories were rejected and later proven wrong. And once you prove that something is wrong or at least highly, highly unlikely, you must think of another possible and more likely explanations and not move on insisting on a fairytale.

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References:

Cobb, M. 2012. The enigmatic Ediacaran biota just got more enigmatic. Or did it? Why Evolution Is True. Available online at <http://whyevolutionistrue.wordpress.com/2012/12/20/the-enigmatic-ediacaran-biota-just-got-more-enigmatic-or-did-it/ >

Retallack, G. 2012. Ediacaran life on land. Nature. DOI: 10.1038/nature11777

Retallack, G. 2007. Growth, decay and burial compaction of Dickinsonia, an iconic Ediacaran fossil. Alcheringa: An Australasian Journal of Palaeontology, 31 (3), 215-240 DOI: 10.1080/03115510701484705

Switek, B. 2012. Controversial claim puts life on land 65 million years early. Nature. DOI: 10.1038/nature.2012.12017

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Why thymine instead of uracil?

by Piter Kehoma Boll

ResearchBlogging.org About a year ago, while I was in my class of Techniques of Molecular Diagnosis, an interesting doubt sprouted: why does DNA use thymine instead of uracil as RNA does?

I hope everybody reading this knows about nucleic acids and the difference between DNA and RNA. As a very quick review:

RNA (ribonucleic acid) is a polymer made of ribonucleotides, compound molecules made of three parts, or smaller molecules: a nitrogenous base (adenine, uracil, cytosine or guanine), a ribose sugar and a phosphate group.

DNA (deoxyribonucleic acid) is similar, but instead of uracil it has thymine, and instead of a ribose sugar is has a deoxyribose, so that it is made of deoxyribonucleotides. Another difference is that DNA is a double chain twisted helicoidally, where two nitrogenous bases (each from one of the chains) are connected. Adenine is always connected to thymine and cytosine always to guanine, so that one chain is always dependent on the other.

Currently it’s highly accepted that RNA was the first nucleic acid to exist and that DNA evolved from it, so the changes in the sugar and one of the nitrogenous bases must have some advantage.

To understand that, let’s take a look at the structure of the uracil:

Uracil

The only difference between it and thymine is the presence of a methyl group at the last one:

Thymine

In fact, thymine is also called 5-methyluracil. But let’s go to the explanation:

While nucleotides are synthesized, the nucleotide-monophosphates (NMPs), i.e., the set nitrogenous base + sugar + phosphate is dehydroxylated, creating 2’-deoxy-nucleotide-monophosphate (dNMPs), i.e., GMP, AMP, CMP and UMP (for guanine, adenine, cytosine and uracil) are changed to dGMP, dAMP, dCMP and dUMP.

This modification by dehydroxylation has been shown to make the phosphodiester bonds (the bonds of phosphates on the sugar) less susceptible to hydrolysis and damage by UV radiation. It assures that a DNA molecule will not be as easy to be broken as an RNA molecule, which is very useful since DNA carries all the information to build up the organism.

After the dehydroxilation of the nucleotide-monophosphates, the next step, catalyzed by folic acid, add a methyl group to the uracil to form a thymine, so turning dUMP into dTMP.

There are many explanations for that:

1. Despite uracil’s tendency to pair with adenine, it can also pair with any other base, including itself. By adding a methyl group (which is hydrophobic) and turning it into thymine, its position is reorganized in the double-helix, not allowing those wrong pairings to happen.

2. Cytosine can deaminate to produce uracil. You can see in the picture below that the only difference between them is the change from an O in uracil to an NH2 in cytosine. The problem is that, if uracil were a component of DNA, the repair systems would not be able to distinguish original uracil from uracil originated by deamination of cytosine. So using thymine instead makes it way easier and more stable, as any uracil inside DNA must come from a cytosine and so it can be replaced by a new cytosine.

Cytosine

This didn’t evolve for that purpose, of course. Evolution cannot predict what happens. Probably during the earliest times of life, eventually an error changed uracil for thymine and it was found to be more stable to carry information, since such a molecule wouldn’t be destroyed so easily and thus would succeed in passing its “layout” to the next generation.

It makes me wonder… Could some alien life form have found an alternative way to deal with RNA’s (or something equivalent) instability?

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Main Reference:

Jonsson, J. (1996). The Evolutionary Transition from Uracil to Thymine Balances the Genetic Code Journal of Chemometrics, 10, 163-170 DOI: 10.1002/(SICI)1099-128X(199603)10:2

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Why I Don’t Trust Jack Horner 2: Why the King deserves his crown

by Carlos Augusto Chamarelli

Hey there again. After the previous article about Jack Horner’s plan to transform chickens into dinosaurs, what’s better than go back to showing contempt for his other theories? So let’s talk about his opinions regarding that one elusive theropod nobody ever heard about: the Tyrannosaurus rex.

Most specifically, about the most heinous and debated of his claims: that T.rex was so ill-suited to be a hunter that he had to live entirely of kills from other predators and was no more than a giant vulture. Understandably not many people were happy with this, and many studies since were made to verify if Horner’s claim were true. With mixed results, but not that stopped some to agree with him.

In reality he wasn’t the first to try and discredit T.rex of his predator status; back in 1917, paleontologist Lawrence Lambe concluded Tyrannosaurus couldn’t be a predator because Albertosaurus (yeah, I don’t know either) teeth did not show any sign of wear, which soon enough was pointed out as BS because theropods constantly changed their teeth throughout their lives. So T.rex continued to enjoy his status as the supreme predator he’s cracked to be and the scavenger theory was mostly left aside.

I’m not sure when Horner first proposed T.rex was a scavenger, but his opinions were already present during the early 90’s; during the production of Jurassic Park, in which he was one of the paleontological consulters, he stated that T.rex should be depicted as such. Fortunately, everybody knew better and made him a hunter like Bakker suggested, and we could see the creature in all his glory in the first two movies of the series.

You people, I don’t care if it’s outdated and full of inaccuracies; this is the only place where dinosaurs genuinely feel like they’re real things. Screencap of Jurassic Park. Extracted from jurassicpark.wikia.com

Until the early 2000’s that is, when Horner’s theory came in full power to the public. His TV-special “Valley of the T.rex” was entirely devoted to show the creature as a stinky scavenger, and during the production of Jurassic Park 3, Bakker knew better than participate of this train wreck, leaving the movie at the mercy of Horner as its sole consulter…

And from there, everything went downhill. Screen cap of Jurassic Park 3. Extracted from gonemovie.com.

As Wikipedia so nicely resumes for us, the main aspects that Horner uses to rationalize the idea of T.rex as a scavenger are as follow:

- Tyrannosaur arms are short when compared to other known predators. Horner argues that the arms were too short to make the necessary gripping force to hold on to prey.

- Tyrannosaurs had large olfactory bulbs and olfactory nerves (relative to their brain size). These suggest a highly developed sense of smell which could sniff out carcasses over great distances, as modern vultures do.

- Tyrannosaur teeth could crush bone, and therefore could extract as much food (bone marrow) as possible from carcass remnants, usually the least nutritious parts.

- Since at least some of Tyrannosaurus’s potential prey could move quickly, evidence that it walked instead of ran could indicate that it was a scavenger.

That said; let’s take a closer look at each of these points, shall we?

- Arms

Ah yes, T.rex arms. Those sorry excuses for limbs are the trademark of the king and his kin. Completely out of proportion and with only two fingers, it’s easily one of its most puzzling characteristics as many theories and no agreement exist about their real utility; ranging from a prosaic, moderately believable but ultimately flawed use like lifting his body when the animal was lying down, to the most reason defying such as picking his teeth or holding struggling prey.

At least it makes him easy to impersonate. Extracted from blogs.smithsonianmag.com

But I do believe the answer is in fact quite simple, but lots of people will be outraged exactly because of that.

Nothing.

T.rex most likely didn’t use them for anything because, well, it didn’t need. They were in a process of atrophy*. It’s really sad that the only mention of such occurrence is usually attributed to the outdated theory of Lamarckism, with the law of use and disuse, because, in a way, that’s kind of what happens.
To understand it better: you know that evolution work by mutations, right? They occur at random in the process of reproduction, but as the model always goes, if said mutation proves to be an advantage for that individual, he has higher chances to pass on his genes for the next generations. But sometimes, things go in a different direction.

Let’s make this one model with two different species, a caveman and a T.rex.

Why yes, MS Paint & MS Word work just fine for me. Picture by yours truly.

The caveman is like your average caveman: he has two legs, two arms, a head and a big, spiked club. The T.rex, on the other hand, is actually an ancestor form which have long arms, fictionalized for the sake of the explanation**, he’s like “cool, I can grab things with these, but my mouth already does everything I guess”.

Now say that they both at some point had offspring with mutations that affect their forelimbs, making their arms dwindle and become useless. For the cavemen, this could be fatal since he relies on his hands to grab things, make tools, maybe even socializing, so the natural conclusion is that this bad gene results in a dead caveman who never stood a chance to have children. For the T.rex, his tiny arms doesn’t affect him as much, because his jaws do all the work of killing prey and fighting rivals, which means he can survive normally and pass on his “bad” genes and create an entire dynasty of short-armed dinosaurs.

Putting a magnolia flower on her head is the way to tell she’s a female. Also, poor caveman. Picture by yours truly.

In other words, if a mutation doesn’t have a big impact in the creature’s lifestyle, it probably will carry on to next generations until the whole species has it. Among some examples where this happened we can cite snakes and other legless reptiles (which became, you guessed it, legless), primitive tetrapods (which lost fish characteristics such as fins) and even us humans (which lost our tails).

Degenerated arms are not even an exclusivity of tyrannosaurids; other dinosaurs had similar occurrences, from the small, one-fingered alvarezsaurids such as Linhenykus (whose arms were more like pointed stubs) to giant Abelisaurids, the “T.rexes of the south hemisphere”, so to speak. The latter, in fact, had much more pathetic-looking limbs than T.rex.

I mean, really, what the heck, nature? Carnotaurus skeleton mount from the Chlupáč museum in Prague. Extracted from http://commons.wikimedia.org

There were also the famous terror birds, which appeared in the Cenozoic; these too were large-sized predators with beaks as deadly as their wings where shamefully small. The logical conclusion with all of this is that arms for bipedal predator dinosaurs are overrated, and the fact T.rex had tiny arms as he did is completely irrelevant as evidence for scavenging habits.

Unless you think they were ALL scavengers, but… Why would you think that? Picture by Zdenek Burian.

- Senses

Remember that one scene in Jurassic Park where the T.rex escapes and Grant has to save Hammond’s grandchildren and they stand perfectly still because then the T.rex couldn’t see them? Of course you do, you read about it everywhere how it’s bonkers because he could have smelled them: T.rex had an exceptional sense of smell, just one more of his claims to fame.

Pictured: Bonkers. Screencap of Jurassic Park. Extracted from lost-world.com

T.rex’s sense of smell is thought to be surpassed only by the modern day turkey vulture (Cathartes aura), which is all too convenient to Horner’s theory, right? Except having a good sense of smell is just as useful for hunting animals, as proved by modern canids and felines. “But, PK, those are mammals, we’re talking about dinosaurs! They’re closer to birds!” you might say, but that’s alright, because contrary to what many might believe thanks to the super-sniffing vultures, some non-scavenger birds do have a good sense of smell.

The majority of them use it to detect predators, but there are some species that use it to hunt prey, like the kiwi birds, whose nostrils are so long they actually go all the way to the tip of the beak, excellent for sniffing worms underground.

It is fair compare it with T.rex, right? Right? Extracted from rmagibess.wordpress.com

But even more bonkerous is the fact that, never mind his extraordinary olfaction, he COULD see them!

It’s not always apparent, because most of the time you see pictures of T.rex’s skull in profile, but if you have the chance to look at one from the front, you’ll see that the hind part of the skull is actually visibly wider than the snout, causing the eyes to face forward rather than the sides as it’s more commonly seen in dinosaurs; it’s also at a higher level than the snout, giving it a clearer view and the distinctive shape.

It’s also kinda hard to find such picture, specially one that haven’t been seen around a thousand times. Sue’s skeleton mount at the Chicago Field Museum of Natural History. Extracted from wikipedia.org… Do I even need to say that?

Eyes facing forward are a characteristic of animals with good eyesight, such as primates and birds of prey, with the owls being the ultimate example of this; the binocular vision provided is essential for calculating distances better and maintain focused on targets. So that’s a tricky question: if T.rex was a purely a scavenger, then why did it had eyesight akin to predatory birds who are such efficient hunters?

- Teeth and jaws

Tyrannosaurids are an interesting lot when it comes to teeth. Usually, carnivore dinosaurs have slicing teeth shaped like steak knives, efficiently tearing the flesh out of the victim’s bone. T.rex, on the other had, had teeth at one point described as “deadly bananas”: they where thick and with very deep roots, which made them incredibly strong.

Those are medium sized, by the way. Extracted from discovery.com

In addition, their jaws were also different: the classic model has the jaws roughly the same width; while in T.rex the upper jaw was wider, giving him the characteristic overbite appearance, which allowed him to stress bones in such a way that they could easily crack them.

On top of that, T.rex is thought to have had the most powerful bite in the dinosaur world. How powerful it was? The most recent study, released this year, indicates around 30,000 and 60,000 Newtons. To puts things in perspective, the previous study pointed up to 13,000 Newtons,  enough to crush a car. That being said, I’m not surprised if someone told me that if a T.rex and a tank were in a fight, the dinosaur would’ve won.

Once again the internet proves it has everything. Extracted from nebomusic.net

But once again, this isn’t an indicative that T.rex was purely a scavenger, since powerful bites aren’t unique to such behavior. Think of the jaguar (Panthera onca), which isn’t one of the largest big cats out there, but even for its size it has an unusually strong bite that can crack even a man’s skull, and is the apex predator of its habitat.

Hypothetically speaking, if jaguars were to evolve into much larger species, then forms with even stronger bite power could appear. For a creature as big as T.rex, this could be one such scenario; their ancestors could be like the jaguar in size and potency, but things went out of hand and produced a big animal with an insanely strong bite, and being able to feed on bone marrow was just an appreciated bonus.

So anyways, remember that scene in Jurassic Park 3? Yes, THAT scene…

So many bad words were uttered directed at this. Screencap of Jurassic Park 3. Extracted from djgomasar.blogspot.com.b

IT WAS TOTAL BS!

The first bite to the neck would’ve been enough to kill the Spinosaurus. See, that’s one reason that makes T.rex lives up to its title: it doesn’t matter if Spinosaurus or Giganotosaurus or any other theropod was larger than him, his absurdly powerful bite would be more than able to overpower them.

But no, Horner had to have things his way and cheated by okaying them into making a Spinosaurus on steroids not care about fish and fight a sub-adult T.rex and survive a bone-crushing bite to the neck. Sorry about that little rant, but it’s all just too unnerving to see such gratuitous mockery of paleontology in one place.

SO MANY. Screepcap of Jurassic Park 3. Extracted from villains.wikia.com

- Legs and body build

Paleontologists have divergent opinions about the overall build of Tyrannosaurus; two body models commonly followed are the bulky type and the athletic type. The bulky body implies a slow-moving creature with a more limited ability to run, some might say one that would be unable to chase its prey, while the athletic body implies an active running creature.

Paleontologists who support the athletic type suggest that, despite it’s size, the overall proportion of the legs of the T.rex are more characteristic of a running animal, in other words, T.rex was very much able to catch up with its prey in a chase. So naturally this is what makes the most sense if you want to show T.rex as a hunter.

“Look, a Velociraptor!”. Sue’s skeleton again. Extracted from cmnh.org

My opinion? He was a bulky type.

“Say what?”

In reality, nobody is quite sure of how fast Tyrannosaurus was, but from analysis and calculations an estimative can be made, but even those don’t really support the image of T.rex running at overly high speeds as usually shown.

In a optimistic scenario, the top speed for T.rex is somewhere around 30 km/h (18 mph) at best, which isn’t terribly fast. I’ve read about some estimatives being over twice this value, but that seems more like an exaggeration to argue with Horner’s theory in the wrong direction.

Because the larger the creature becomes, the more heavily built it has to be in order to support its own weight, there’s a limit on how light the creature can be until it become too big and heavy to support itself, so a large bipedal creature like T.rex probably needed to have a solid build in order to stand in their feet. Not to mention that, in order to be able to run at the suggested exaggerated speeds, much of its body mass would have to be in their legs muscles.

Whoever, being slow doesn’t rule out the possibility of Tyrannosaurus being a hunter; he maybe just had a different approach. Instead of focusing in speed, Tyrannosaurus could be a robust creature built primarily for strength. Why would did he need to be so? Well, what manner of prey did he had available in his domain?

Spikes, spikes everywhere. Pictures by John Sibbick. Extracted from http://fineartamerica.com

Why, just the most dangerous herbivores ever to appear in the Mesozoic era.

Nobody can attribute speed as a quality of ankylosaurids; they had a solid build, covered in heavy armor and short legs for better standing their ground.

Ceratopsians, despite what most reconstructions tend to show, were probably very poor runners: their forelimbs weren’t even appropriate to run, (I intend to talk about this in a future post) so they probably relied more in numbers and their own weaponry for survival than making a dash for it. So if being fast wasn’t needed to catch its prey, the best option would build up endurance, and the apparent running legs of T.rex would be more like a way to trade speed for strength without being completely handicapped.

Meaning the T.rex wasn’t a creature made to pursue its prey. No sir. He was juggernaut made to stay there and fight them, and win. Somehow pure raw strength could prove to be a better strategy than speed to overcome a well armed opponent.

Suddenly this setup makes a lot of sense. Picture by Charles Knight.

While the T.rex could be injured or even killed by his prey, he could also finish it just as easily: biting the head or the backs would have shattered their bones and leave the prey paralyzed in the best of hypothesis, while just ripping a chunk could leave a fatal wound. In this scenario, T.rex’s eyes would then be an invaluable asset to focus on their prey during the fight, rather than be used during a chase. And if he ever needed to run, it would be more like walking real fast.

In a way, one can think that ceratopsians and ankylosaurus where in a mutual armed race with tyrannosaurids, each developing even more powerful weapons against each other: they seemed to be found primary where those types of herbivores thrived (i.e. North America and Asia), and their evolution is somewhat consistent with the appearance and ascension of those herbivores. Now consider this: despite the duckbilled dinosaur’s fame as widespread, they were actually outnumbered by ceratopsians, which means something must have been preying on them to keep their numbers, right?

Oc course, that’s my personal opinion, I might be wrong: there’s no evidence of ankylosaurids with signs of predation yet, but I’m not convinced absolutely nothing would attack them if given the chance, specially something with a bite like T.rex.

And to think for the longest time museums didn’t like those kind of findings because they were “no good for exhibition”. Triceratops sacrum with T.rex bite marks. Extracted from palaeocritti.com

While there’s evidence that T.rex preyed on both hadrosaurids and ceratopsians (i.e. some show teeth perforations while others healed bite marks in bones that could only be possible if the dinosaur was alive), it’s safe to assume that the horned dinosaurs were his chief prey, at least to the fully mature individuals.

While there’s no official estimative on how fast hadrosaurids could run, it’s certain that they were faster than an adult T.rex, but if it’s true that they could also hunt in packs to a degree, then it could be an explanation for this finding. Alternatively, younger individuals could have preyed on hadrosaurids if they were light built. But even more impressive seem to be the fact that something actually could survive an T-rex attack.

-Anything else?

Actually yes, there’s one more point beyond the ones listed: Energy efficiency.

Modern scavengers like vultures and jackals are allowed the luxury having this lifestyle because they’re small and can cover a large area without wasting too much energy (i.e. vultures are soaring birds, meaning they are able to maintain flight without flapping their wings).

A large creature like T.rex would be doomed to extinction if it was an obliged scavenger because he would probably run out of energy trying to locate the next meal, and even then he has to hope there’s enough left to eat and no other T.rex claimed it already, not to mention this unviable lifestyle would make their population be massively reduced in order to be able to support just a handful of these dinosaurs

So there you have it. Tyrannosaurus might not have been the largest carnivore to ever exist, but he certainly was the most powerful. Despite all those evidences, there’s a consensus among those who support the hunting behavior of T.rex that he was an opportunistic hunter. That is, while he could very well kill his own prey, he wasn’t above stealing or eating carcasses. It’s a free meal after all.

In the end, this is what the whole problem is about: Horner didn’t take in account that the evidence he used to support his theory also had explanations that indicated the opposite. Just to make things clear with the “Why I Don’t Trust Jack Horner” series: while I don’t think he’s a bad paleontologist, I do believe he’s a little misguided about his recent theories. And quite frankly, I’m pretty sure that if Horner went back in time and was face-to-face with the creature he’s sure was a scavenger, he would NOT just stand there calmly.

Thanks for reading!

* Because once the first degeneration took place, nothing would stop it from being further degenerated by a subsequent mutation.

** Early tyrannosaurids did have longer arms, but in the model the dinosaur is already in its later form to illustrate that even a sudden mutation, as opposed to a gradual one, still wouldn’t affect it.
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References & Further Reading:
Erickson, Gregory M. 2005. ‘Um Sopro de Vida no Tyrannosaurus rex’. Scientific American Brasil – Edição Especial: Dinossauros e Outros Monstros.

Wikipedia. Tyrannosaurus. Available on-line in: <en.wikipedia.org/wiki/Tyrannosaurus>. Acess on May 15th, 2012

BBC – T. rex bite was world’s strongest. Avaiable online at: <http://www.bbc.co.uk/nature/17159086&gt;

Science Daily- Birds Can Detect Predators Using Smell. Avaiable online in: <http://www.sciencedaily.com/releases/2008/04/080427233813.htm&gt;

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If you like flowers, you should love insects

by Piter Kehoma Boll

ResearchBlogging.orgEverybody likes flowers, right? They are so colorful and beautiful and usually have a wonderful scent. People love to have them in their gardens and women love to receive a nice flower bouquet from their boyfriends.

Some flowering plants, from left to right: Rosa ‘Hybrid Tea’, Pachystachys lutea and Zinnia elegans. All photos by Piter K. Boll (i.e. myself!)*

But why are flowers so beautiful? Of course the flowers seen above are derived from varieties artificially selected by humans to increase their beauty, but flowers in nature are wonderful too!

Naturally occuring flowers. From left to right: Oxalis sp., Ipomoea fimbriosepala and Zephyranthes robusta. All photos again by myself (Piter K. Boll)*

Surely that beauty is not intended to please people or whatever. That’s totally nonsense and just some religious people could have such a wrong idea. If plants have nice flowers, it must give them some advantage.

As everybody knows (at least I hope so), plants usually cannot move like animals, so they are condemned to stay still on their spot. That can mean a lot of trouble when you are looking for resources like water, light or basic elements like nitrogen. So evolution leads to the rising of amazing structures to make plants survive, like getting a hard stem to become taller or developing smaller or larger leaves, thorns, tendrils or even becoming carnivorous. But plants also need to reproduce and for that they need a mate, but since they are attached to the substrate, they have to find alternative ways to join their gametes.

Most primitive plants manage to do that through water or wind, just letting their reproductive structures go and hoping that they will reach their destination. As you can see, this method is not the best one, since fertilization occurs totally by chance. Besides that, these ways are limited regarding to the places where they are successful. A plant fertilized through water needs to be inside water or live close to the ground on places where it eventually get submersed; the same way, a plant which relies on the winds needs, of course, to be where the wind blows.

Moss (left) relies on water to reproduce, while conifers (right) need wind. Once more, photos by Piter K. Boll. *

Those methods, though limited, worked well enough for millions of years until sometime in the Cretaceous period, when a group of animals started to diverse astonishingly: the insects.

Insects are small and prolific. They have a hard outer skeleton of chitin, which prevents dehydration and injuries, and many of them learned to fly, so being able to cross large distances and colonize new habitats.

Insects existed, of course, at least since the Carboniferous. The most famous of them is the giant dragonfly Meganeura. But during the Cretaceous those groups that today are the most diverse started to appear in fossils: ants, bees, termites, butterflies, moths, aphids and grasshoppers. Beetles, the most diverse group of insects today (containing more species than all other arthropods together) are found in fossils since the Carboniferous, but almost went extinct during the Permian-Triassic boundary that marks the most terrible mass extinction on Earth. After this tragic event, they stayed more discrete until a boom in diversification in Cretaceous together with the already mentioned insects.

Well, all those insects needed to eat like anything else and started to feed on plants, including their pollen. That could have been a serious trouble, but plants managed to deal with it by modifying themselves in a way that the insects now became something useful to them. If insects were attracted to their pollen, why couldn’t they carry it to other plants, so assuring a more secure fertilization?
That’s exactly what plants made, but in order to attract insects even more to their reproductive organs, those started to increase in size and get nice colors. It all happened through natural selection of random mutations, of course. No one is assuming that plants or insects actually chose to change, that’s nonsense. What I’m trying to say (through a simpler way) is that those plants that were able to attach some of their pollen grains to insects, so that it reached other plants that the insect visited, were more successful to reproduce. The same way, those plants with more beautiful flowers attracted more insects and were also more successful to reproduce.

Anyway, that’s why we should thank insects for existing, since without them we wouldn’t have so nice flowers to decorate our lives. And if you like flowers but hate insects, well, you are being extremely unfair to nature.

I know that some may say “but I like butterflies. They are beautiful and cool and cute and they pollinate everything, so I just need to like these insects and not all those disgusting things.”
Oh, really? So you like butterflies? I’m sure you like this one:

Caterpillar of Agraulis vanillae. Photo by Bill Frank extracted from jaxshells.org

Most people like butterflies and hate caterpillars, but they are exactly the same thing. And actually these insects spend most of their life as a larva. Now just to satiate your curiosity, this is what that caterpillar looks like as an adult:

An adult of Agraulis vanillae on a head of Zinnia elegans. Photo by Piter K. Boll.*

But butterflies are not the only pollinators and not even the most common ones. Bees, as you know, are also very important and the main pollinators of many economically important plants, especially fructiferous ones. Wasps, flies, mosquitos, scorpionflies and moths are also important, but we cannot forget beetles.

Most basal and primitive angiosperms are pollinated by beetles, so that its more likely that these were the guys behind the appearance and diversification of flowering plants. There are many evidences for that, like an increasing diversity of angiosperms in fossil records being contemporaneous to an increase of beetle species.

Recently, some fossil flowers from the Turonian age (about 90 million years old) were found in Sayreville, New Jersey. Those were called Microvictoria svitkoana due to their astonishing similarity to the giant Amazon water lily, Victoria amazonica, even though much smaller in size.

Flower of Victoria amazonica, one of the most primitive angiosperms. It’s easy to notice that it still resembles somewhat a conifer cone. Photo by Frank Wouters, extracted from commons.wikimedia.org.

Despite primitive, it’s certainly a very beautiful flower, and it can only exist thanks to beetles of the genus Cyclocephala, like this one.

Cyclocephala hardyi, a beetle that pollinates Victoria amazonica. Photo extracted from ssaft.com/Blog/dotclear/

What do you think about it? It’s actually a cool pal, isn’t it? If you look closer, you may see that every insect is amazing in it own way, even cockroaches!

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References:

Béthoux, O. 2009. The Earliest Beetle Identified. Journal of Paleontology, 83 (6), 931-937 DOI: 10.1666/08-158.1

Crepet, W. L. 1996. Timing in the evolution of derived floral characters: Upper Cretaceous (Turonian) taxa with tricolpate and tricolpate-derived pollen. Review of Palaeobotany and Palynology, 90, 339-359 DOI: 10.1016/0034-6667(95)00091-7

Gandolfo, M. A., Nixon, K. C. and Crepet, W. L. 2004. Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early Angiosperms. PNAS, 101 (21), 8056-8060 DOI: 10.1073/pnas.0402473101

Seymour, R. S. and Matthews, P. G. D. 2006. The Role of Thermogenesis in the Pollination Biology of the Amazon Waterlily Victoria amazonicaAnnals of Botany, 98 (6), 1129-1135 DOI: 10.1093/aob/mcl201

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What’s a species 2: Vertical species concepts

by Piter Kehoma Boll

Hello, guys!

I finally decided to go on and write the second part of my article about species concepts. You can see the first part here, where I talked about horizontal species concepts. Today I’m going to talk about the other perspective, the vertical species concepts, which are based on lineages, i.e., how species happen through time.

Vertical concepts are hardly used to actually define a species, since they do not represent the current situation of living beings and it’s hard to know the real history of a population to determine its status through all his existence. However these concepts are useful in phylogenetic reconstructions and to understand how new species arrive from others through time.

Well, let’s see the two main vertical species concepts.

1. Cladistic species concept

Proposed by Ridley in 1989, it defines a species as a set of organisms between two speciation events, or between one speciation event and one extinction event. According to this, a species comes to exist when a lineage of organisms is split in two. There are no paraphyletic species in this concept, since when a speciation event occur, the ancestral species becomes extinct, giving rise to two new species.

Cladistic concept: every time a speciation event occur, two new species are created and the ancestral species becomes extinct.

2. Evolutionary species concept

An evolutionary species is defined as a set of organisms from a single lineage that has its own evolutionary tendencies and historical fate. Differently from the cladistic species, the evolutionary species does not necessarily become extinct when another lineage split from it, so being able to be paraphyletic, i.e., if a population is divided in two, the one that continues to have the same general features and the same evolutionary path is considered the same species as the ancestral one.

Evolutionary concept: a species does not necessarily become extinct during a speciation event. Species 1 is paraphyletic after split from species 2.

Since there is no record of the evolutionary history of organisms, there is no way to determine it for any species. Some ideas may be proposed and highly supported by genetic analyses, but we can never know for sure how things really happened, so that vertical concepts cannot be applied practically and are more useful to infer genetic relationships between different populations and so guide their correct management in conservation efforts.

Another point is that by vertical concepts, two organisms are considered separate species as soon as they move on in different lineages, in different populations that will not come in touch again, so that even two cousins would be different species, even though genetically, morphologically and ecologically very similar.

So vertical concepts are more useful to determine phylogeny and help in population genetics, but not to actually define species in any ecosystem, since in this case the situation is characterized by the present status of organisms and so better supported by horizontal approaches.

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References:

Mayden, R. L. 1997. A hierarchy of species concepts: the denoument in the saga of the species problem, in M. F. Claridge, H. A. Dawah and M. R. Wilson (eds.), Species: The units of diversity, London: Chapman and Hall, 381-423

Ridley, M. 2004. Evolution. Blackwell Publishing. ISBN 1-4051-0345-0.

Stamos, D. N. 2002. Species, languages, and the horizontal/vertical distinction. Biology and Phylosophy, 17, 171-198.

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