Paleoblog reports on a Science paper that contends relationships between some of the major animal phyla (body types).
Amongst other results are:
- hypothesising a clade of moulting animals (previously defined as Ecdysozoa;
- relating lophophorates (three small marine phyla) to annelids and molluscs
- molecular confirmation of the monophyly of molluscs;
- supporting velvet worms rather than tardigrades as closes phylum to arthropods;
- hypothesising a clade uniting annelids, brachiopods, nemerteans and phoronids (mainly small marine phyla);
- ctenophores (comb jellyfish) as the earliest diverging multicellular animal of existing phyla.
This last result I find most interesting - that ctenophores diverged earlier than sponges, which were arguably closest in broad morphology to the ediacarans that preceded the Cambrian era from which emerged modern phyla. This newly attributed status of the comb jellyfish has filtered through to reportage in the mainstream press.
The authors analyse about 40 Mb of "expressed sequencing tags" from 21 phyla, including 11 for which the data had not previously been available. This is a form of molecular (genetic) analysis.
The pedigree of the sources is good. I am not sufficiently knowledgeable about the science, so I can only report the findings. There's a lot to digest.
Showing posts with label taxonomy. Show all posts
Showing posts with label taxonomy. Show all posts
Sunday, April 13, 2008
Wednesday, March 26, 2008
Surviving early mammal lineages
Researching mammals seems to be a particularly popular occupation. Most of that research relates to extant species and their evolutionary history. So it's mostly eutherians (placentals), metatherians (marsupials), and monotremes. It's hard to find much detail about extinct lineages such as New Zealand's mysterious SB mammal fossil.
I'm currently browsing with curiosity a hefty tome called Mammals From The Age Of Dinosaurs. It's about as comprehensive as one can get, and is destined to be the reference book for early mammals. Written by three of the leading experts (and most widely quoted) in the field of mammal paleontology: Zofia Kielan-Jaworowska, Richard Cifelli, and Zhe-Xi Luo. It's dated 2004; to get anything more current, you'd have to be constantly scouring the journals (which is not a bad thing, as these are times of rapid change in knowledge and understanding in this field.)
The book contains many seminal reference points, including a full survey of distribution by location and period (to just past the Mesozoic boundary), and a fully detailed survey of each major lineage of the Mesozoic.The diagrams I find particularly useful are - two (alternative) cladograms of all major mammal taxa up to eutheria (pp521 & 522); - an overview of the changed view of the evolution of the major lineages (p5); - most importantly, a diagram of the temporal distribution (through the Mesozoic) and relationships of the main lineages (p3); - a clade table (listing) of all lineages down to family level (pp 14-15).
Of major interest is the comment (p13) that only four major lineages have a significant presence after the KT boundary (end of the Mesozoic, and the dinosaurs).
Four? To the extant lineages mentioned above, the book adds multituberculates (p15). In a footnote, they elaborate the list with the multituberculate suborder Cimolodonta (lasting to the Eocene), and one dryolestoid from the Paleocene of South America. However, that note is not complete, as there are scatterings of other multituberculate taxa that are mentioned as passing through to the Paleocene. These include Ptilodontidae, and Gondwanatheria. The latter are admitted as uncertain placement (Incertae sedis) - somewhere between monotremes and (metatherians plus eutherians) - but discussed with multituberculates.
Ptilodus, a Ptilodontid
[Update 27-Mar: Dryolestes is Trechnotherian - a clade (a superset of both eutherians and metatherians) which covers all mammals that give birth to live young. I'll now exclude these from the discussion, since I'm focusing on egg-laying mammals, which it looks like the SB mammal is.]
So far, then, we have three non-therian - egg-laying - groupings surviving into the Paleocene (which ended 55 million years ago): Monotremes, multituberculates and, arguably, Gondwanatherians. To this, we now add the even more enigmatic SB mammal, surviving all the way to the Miocene, 19mya.
So what does this say about the SB mammal?
On the one hand, Worthy et al place this mammal in an unresolved trichotomy with multituberculates (which it says are more basal) and the more derived clades that include (Tinodon + the viviparous therians). In effect, pretty close to multituberculates, but no match. On the basis of the femur fragment (specifically, the greater trochanter), it's more primitive than the latter - but that's predicated on the femur and jaw fragments matching. Parsimony suggested so, but it's not a guarantee.
On the other hand, the paucity - and piecemeal nature - of the book's references to non-therian KT survivors is a good reminder that we are dealing with a matching scarcity of pertinent fossils. What has been reported so far should not be taken as a complete and reliable guide to what did survive. New Zealand has, after all, sheltered such oddities as the lizard-like Tuatara and the Leopelmatid frog, no less surprising in their uniqueness.
Next up: more on multituberculates.
References
Kielan-Jaworowska Z, Cifelli R L, and Luo Z-X (2004): Mammals from the age of dinosaurs : origins, evolution, and structure. New York, Columbia University Press.
Worthy T, Tennyson A, Archer M et al (2006): Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific in PNAS vol 103 no 51.
I'm currently browsing with curiosity a hefty tome called Mammals From The Age Of Dinosaurs. It's about as comprehensive as one can get, and is destined to be the reference book for early mammals. Written by three of the leading experts (and most widely quoted) in the field of mammal paleontology: Zofia Kielan-Jaworowska, Richard Cifelli, and Zhe-Xi Luo. It's dated 2004; to get anything more current, you'd have to be constantly scouring the journals (which is not a bad thing, as these are times of rapid change in knowledge and understanding in this field.)
The book contains many seminal reference points, including a full survey of distribution by location and period (to just past the Mesozoic boundary), and a fully detailed survey of each major lineage of the Mesozoic.The diagrams I find particularly useful are - two (alternative) cladograms of all major mammal taxa up to eutheria (pp521 & 522); - an overview of the changed view of the evolution of the major lineages (p5); - most importantly, a diagram of the temporal distribution (through the Mesozoic) and relationships of the main lineages (p3); - a clade table (listing) of all lineages down to family level (pp 14-15).
Of major interest is the comment (p13) that only four major lineages have a significant presence after the KT boundary (end of the Mesozoic, and the dinosaurs).
Four? To the extant lineages mentioned above, the book adds multituberculates (p15). In a footnote, they elaborate the list with the multituberculate suborder Cimolodonta (lasting to the Eocene), and one dryolestoid from the Paleocene of South America. However, that note is not complete, as there are scatterings of other multituberculate taxa that are mentioned as passing through to the Paleocene. These include Ptilodontidae, and Gondwanatheria. The latter are admitted as uncertain placement (Incertae sedis) - somewhere between monotremes and (metatherians plus eutherians) - but discussed with multituberculates.
Ptilodus, a Ptilodontid[Update 27-Mar: Dryolestes is Trechnotherian - a clade (a superset of both eutherians and metatherians) which covers all mammals that give birth to live young. I'll now exclude these from the discussion, since I'm focusing on egg-laying mammals, which it looks like the SB mammal is.]
So far, then, we have three non-therian - egg-laying - groupings surviving into the Paleocene (which ended 55 million years ago): Monotremes, multituberculates and, arguably, Gondwanatherians. To this, we now add the even more enigmatic SB mammal, surviving all the way to the Miocene, 19mya.
So what does this say about the SB mammal?
On the one hand, Worthy et al place this mammal in an unresolved trichotomy with multituberculates (which it says are more basal) and the more derived clades that include (Tinodon + the viviparous therians). In effect, pretty close to multituberculates, but no match. On the basis of the femur fragment (specifically, the greater trochanter), it's more primitive than the latter - but that's predicated on the femur and jaw fragments matching. Parsimony suggested so, but it's not a guarantee.
On the other hand, the paucity - and piecemeal nature - of the book's references to non-therian KT survivors is a good reminder that we are dealing with a matching scarcity of pertinent fossils. What has been reported so far should not be taken as a complete and reliable guide to what did survive. New Zealand has, after all, sheltered such oddities as the lizard-like Tuatara and the Leopelmatid frog, no less surprising in their uniqueness.
Next up: more on multituberculates.
References
Kielan-Jaworowska Z, Cifelli R L, and Luo Z-X (2004): Mammals from the age of dinosaurs : origins, evolution, and structure. New York, Columbia University Press.
Worthy T, Tennyson A, Archer M et al (2006): Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific in PNAS vol 103 no 51.
Sunday, March 16, 2008
Paucity of useful books on mammals
A quote from a 1993 book called Mammal Phylogeny:
"Prior to the advent of phylogenetic systematics... the influence of environment over natural selection was virtually the only mechanism invoked to describe morphological patterns discovered in the history. It was argued that similar environmental demands... led to the convergent evolution of 'mammalian' characters in many different lineages. Implicit in many discussions is the thought that convergence was so prevalent that the true genealogy could never be known with any precision.Phylogenetic systematics has turned our attention from many of these issues. The discovery of monophyletic taxa replaced definitions of grades as the central issue in understanding early mammalian history." (pp130-131; my emphasis).
It goes on to say there is no doubt mammalia is monophyletic. Further: "Previous views saw taxa as classes defined by characters, while contemporary phylogenetics views taxa as individuals defined by common ancestry".
This gives some context to the difficulty I had in finding useful books on mammalian evolution in the university library (UNSW). Most of them were not recent enough to encompass the revolution in evolutionary analysis. One of the more promising titles had an unpromising date from the 1960s, last updated 1972.
The quote above suggests the cladistic approach to analysis has cleared the decks, so to speak. On the one hand, the attempt to group all species into equivalent hierarchical sets was obviously thoroughly doomed. This, even apart from the quite vexed issue of delineating evolutionary lineages into species in the first place.
On the other hand, systematic phylogeny has immeasurably clarified evolutionary relationships, which to my mind should be rather paramount.
On the other, other hand, I can greatly empathise with adherents of Linnean taxonomy, whose tidy world is so greatly threatened. But they should acknowledge the appropriateness of the threat: phylum, order, class, family, and species were always arbitrary, and give unhelpful illusions of equivalence that just do not exist.
Another difficulty for me with libraries is the sort of books I'm looking for: non-therians, that is mammals that are not placental (which also excludes marsupials). Most evolutionary biologists happen to be very much focused on extant species and lineages. Thus most books on mammalian history treat eutherians or metatherians - or monotremes at a pinch.
Reference
Szalay, F, Novacek, M and McKenna, M (eds.) (1993): Mammal Phylogeny. Springer, New York.
"Prior to the advent of phylogenetic systematics... the influence of environment over natural selection was virtually the only mechanism invoked to describe morphological patterns discovered in the history. It was argued that similar environmental demands... led to the convergent evolution of 'mammalian' characters in many different lineages. Implicit in many discussions is the thought that convergence was so prevalent that the true genealogy could never be known with any precision.Phylogenetic systematics has turned our attention from many of these issues. The discovery of monophyletic taxa replaced definitions of grades as the central issue in understanding early mammalian history." (pp130-131; my emphasis).
It goes on to say there is no doubt mammalia is monophyletic. Further: "Previous views saw taxa as classes defined by characters, while contemporary phylogenetics views taxa as individuals defined by common ancestry".
This gives some context to the difficulty I had in finding useful books on mammalian evolution in the university library (UNSW). Most of them were not recent enough to encompass the revolution in evolutionary analysis. One of the more promising titles had an unpromising date from the 1960s, last updated 1972.
The quote above suggests the cladistic approach to analysis has cleared the decks, so to speak. On the one hand, the attempt to group all species into equivalent hierarchical sets was obviously thoroughly doomed. This, even apart from the quite vexed issue of delineating evolutionary lineages into species in the first place.
On the other hand, systematic phylogeny has immeasurably clarified evolutionary relationships, which to my mind should be rather paramount.
On the other, other hand, I can greatly empathise with adherents of Linnean taxonomy, whose tidy world is so greatly threatened. But they should acknowledge the appropriateness of the threat: phylum, order, class, family, and species were always arbitrary, and give unhelpful illusions of equivalence that just do not exist.
Another difficulty for me with libraries is the sort of books I'm looking for: non-therians, that is mammals that are not placental (which also excludes marsupials). Most evolutionary biologists happen to be very much focused on extant species and lineages. Thus most books on mammalian history treat eutherians or metatherians - or monotremes at a pinch.
Reference
Szalay, F, Novacek, M and McKenna, M (eds.) (1993): Mammal Phylogeny. Springer, New York.
Sunday, March 09, 2008
On classifying velvet worms
New Scientist had an article recently on evolution, by Donald Prothero, a geology professor in California. It was trying to smooth the understanding of evolutionary relationships with ten examples of linkages between taxa at various levels. It seems to be based largely on Prothero's recent book "What the fossils say and why it matters" (Columbia Press). Prothero is often described as a paleontologist (including by Stephen Jay Gould); his books include the paleontological and the geological, although heavily weighted towards the latter.
Yet the first evolutionary example in his article is rather contentious. Additional research on the matter gives some insight into the difficulties of phylogeny and taxonomy.
This example was Onychophora - the velvet worm. This is a phylum with just two families - tropical and southern hemisphere - and 80 to 90 species. Their mode is the damp forest floor; it is hard to know how prevalent they are; they are difficult to count, and when this has been done, they're proven endangered. Yet most species are described only very local to where the type specimen (the official sample against which the species is measured).
Prothero depicts Onychophora as the link between two phyla: arthropods (insects, spiders, crustacea) and nematode worms. The former is unremarkable; they are consistently grouped near arthropods. Yet how near, and the closeness of their relationship to nematodes, seems to be still up for grabs.
Tudge puts them in an unresolved trichotomy between Tardigrada and Arthropoda, which grouping is in turn unresolved against nematodes and nematophora (hair worms).
Palaeos.com gives three alternatives. The first posits them as a sub-phylum of Arthropoda, sometimes lumped with Tardigrada as Lobopoda - yet this is not such a common approach, and they acknowledge the polyphyletic questionmark over that. They also list a 2001 source (Peterson and Eernisse) placing instead another obscure phylum, Chaetognatha (marine worms) between Arthropods and Onychophorans. Thitdly, they mention an alternative (Halanych, 2004) that agrees with Tudge.
Wikipedia puts Onychophora between the nematodes and arthropods, with tardigrades closer to the arthropods.
One thing they all agree on: it was wrong to portray Onychophora as the intermediate between annalids and arthropods. Panarthropoda has been used (as recently as Tudge) to lump Onychophora, Tardigrada, and Arthropoda, but it seems a more currently-accepted super-phylum is Ecdysozoa - which adds a few other phyla, including nematodes as closest to the 'panarthropoda'.
I like a clean cladistic diagram. But the jury's still out, so it won't happen yet. The article's a little simplistic, but a rough consensus does seem to place our two lobopods between arthropods and nematodes.
References
Halanych, KM (2004): The new view of animal phylogeny. An Rev. Ecol. Evol. Syst. 35: 229-256.
Prothero, D (2008): What Missing Link? in New Scientist, 1-Mar-2008.
Tudge, C (2000): The Variety of Life. Oxford University Press, Oxford.
Yet the first evolutionary example in his article is rather contentious. Additional research on the matter gives some insight into the difficulties of phylogeny and taxonomy.
This example was Onychophora - the velvet worm. This is a phylum with just two families - tropical and southern hemisphere - and 80 to 90 species. Their mode is the damp forest floor; it is hard to know how prevalent they are; they are difficult to count, and when this has been done, they're proven endangered. Yet most species are described only very local to where the type specimen (the official sample against which the species is measured).
Prothero depicts Onychophora as the link between two phyla: arthropods (insects, spiders, crustacea) and nematode worms. The former is unremarkable; they are consistently grouped near arthropods. Yet how near, and the closeness of their relationship to nematodes, seems to be still up for grabs.
Tudge puts them in an unresolved trichotomy between Tardigrada and Arthropoda, which grouping is in turn unresolved against nematodes and nematophora (hair worms).
Palaeos.com gives three alternatives. The first posits them as a sub-phylum of Arthropoda, sometimes lumped with Tardigrada as Lobopoda - yet this is not such a common approach, and they acknowledge the polyphyletic questionmark over that. They also list a 2001 source (Peterson and Eernisse) placing instead another obscure phylum, Chaetognatha (marine worms) between Arthropods and Onychophorans. Thitdly, they mention an alternative (Halanych, 2004) that agrees with Tudge.
Wikipedia puts Onychophora between the nematodes and arthropods, with tardigrades closer to the arthropods.
One thing they all agree on: it was wrong to portray Onychophora as the intermediate between annalids and arthropods. Panarthropoda has been used (as recently as Tudge) to lump Onychophora, Tardigrada, and Arthropoda, but it seems a more currently-accepted super-phylum is Ecdysozoa - which adds a few other phyla, including nematodes as closest to the 'panarthropoda'.
I like a clean cladistic diagram. But the jury's still out, so it won't happen yet. The article's a little simplistic, but a rough consensus does seem to place our two lobopods between arthropods and nematodes.
References
Halanych, KM (2004): The new view of animal phylogeny. An Rev. Ecol. Evol. Syst. 35: 229-256.
Prothero, D (2008): What Missing Link? in New Scientist, 1-Mar-2008.
Tudge, C (2000): The Variety of Life. Oxford University Press, Oxford.
Saturday, March 08, 2008
Phylogenetic wallpaper
Amira told me about her vision for what would be a phylogenetic wallpaper: that is, one that lists all organisms cladistically around the wall, showing the evolutionary relationships (and degree of closeness) of everything.
Sounds great - if you're that way inclined, which I am too. I said to Amira that you'd need one that could update - pretty much on the fly - because our understanding of evolutionary relationships is changing all the time. Whereas in the past, taxonomy was based largely on morphology - physical relatedness - this is being broken down by molecular analysis, which is showing up much of our morphological classifications to be "mere" cases of convergent evolution.
Visual technology is such that we're not too far away from being able to "paper" a room with very thin, bendable computer displays. The result would be garish but fascinating. Garish because the technology's not good enough to make it easy on the eyes. Fascinating in that at the fringes you'd be seeing more or less constant movement, ripples of change that reflect ongoing corrections in the tree of life. Then every so often there would be a major cracking like an earthquake, as a fundamental adjustment is made.
Sometimes there are hazes, where differences of opinion result in toggles between different states.
Tomorrow, Amira, I'll go into some of those hazes. A recent article on linkages between arthropods and nematodes, vertebrates and echinoderms, speaks to some top-level cladistic relationships - but these are not without contention.
Sounds great - if you're that way inclined, which I am too. I said to Amira that you'd need one that could update - pretty much on the fly - because our understanding of evolutionary relationships is changing all the time. Whereas in the past, taxonomy was based largely on morphology - physical relatedness - this is being broken down by molecular analysis, which is showing up much of our morphological classifications to be "mere" cases of convergent evolution.
Visual technology is such that we're not too far away from being able to "paper" a room with very thin, bendable computer displays. The result would be garish but fascinating. Garish because the technology's not good enough to make it easy on the eyes. Fascinating in that at the fringes you'd be seeing more or less constant movement, ripples of change that reflect ongoing corrections in the tree of life. Then every so often there would be a major cracking like an earthquake, as a fundamental adjustment is made.
Sometimes there are hazes, where differences of opinion result in toggles between different states.
Tomorrow, Amira, I'll go into some of those hazes. A recent article on linkages between arthropods and nematodes, vertebrates and echinoderms, speaks to some top-level cladistic relationships - but these are not without contention.
Thursday, February 28, 2008
Convergent evolution
This is always such a fascinating subject. Earth's natural history is positively littered with examples of different species that develop remarkable similarities to each other in complete evolutionary isolation.
An easy example is the body shapes of sharks (fish), cetaceans (mammals: whales, dolphins, etc), and ichthyosaurs (porpoise-like reptiles): all evolved fairly similar adaptions for swimming, although a notable difference is the tailfins of cetaceans, giving rise to an up-and-down tail movement, rather than side-to-side for the others. A ready observation would be that they show similar vertebrate adaptions to the similar demands of the environment.
There are so many other examples: similar-shaped and/or similar-functioned animals around the world. Try unrelated fish in the arctic and antarctic waters each with an equivalent anti-freeze-like chemical in their blood, with genetic origins quite unconnected.
Try re-invention of the eye several times. Albeit the squid's, for example, is better engineered than ours, since our retinal nerve endings emerge between lens and retina, making for less efficient vision that the squid's whose nerve endings sensibly emerge behind the retina. Moving ahead of myself in Richard Dawkins' The Ancestor's Tale (currently at p344), Dawkins mentions on p602 an expert in comparative zoology of eyes, Professor Michael Land, who identifies nine independent principles of optical mechanics, "each of which has evolved more than once".
Try the proliferation of parallels between eutherian (placental) mammals and metatherian (marsupial) equivalents. Thylacine and timber wolf skulls, for example are said to be nearly identical, despite being completely unrelated.
An easy example is the body shapes of sharks (fish), cetaceans (mammals: whales, dolphins, etc), and ichthyosaurs (porpoise-like reptiles): all evolved fairly similar adaptions for swimming, although a notable difference is the tailfins of cetaceans, giving rise to an up-and-down tail movement, rather than side-to-side for the others. A ready observation would be that they show similar vertebrate adaptions to the similar demands of the environment.
There are so many other examples: similar-shaped and/or similar-functioned animals around the world. Try unrelated fish in the arctic and antarctic waters each with an equivalent anti-freeze-like chemical in their blood, with genetic origins quite unconnected.
Try re-invention of the eye several times. Albeit the squid's, for example, is better engineered than ours, since our retinal nerve endings emerge between lens and retina, making for less efficient vision that the squid's whose nerve endings sensibly emerge behind the retina. Moving ahead of myself in Richard Dawkins' The Ancestor's Tale (currently at p344), Dawkins mentions on p602 an expert in comparative zoology of eyes, Professor Michael Land, who identifies nine independent principles of optical mechanics, "each of which has evolved more than once".
Try the proliferation of parallels between eutherian (placental) mammals and metatherian (marsupial) equivalents. Thylacine and timber wolf skulls, for example are said to be nearly identical, despite being completely unrelated.
It sounds like a rash of grossly unlikely coincidences, ready-made for creationists to fan argumentative flames. Yet in some ways it makes perfect sense: evolution is about species expanding to fill environmental niches, and
a) Over many times and locations, there are sets of all but identical niches
b) What developed and survived was what was most successful in the environment, so the directive forces of nature operated in a similar way on what was often a relatively similar genetic material.
This is obviously quite a source of frustration for taxonomy. Whereas in the relatively recent past, classification was based largely on morphology (body shape and features), modern molecular analysis has demonstrated that many of the connections drawn in the past were examples of convergence.
Dawkins also describes three different moles. The African golden mole (Chrysochloridae) was grouped with the Eurasian mole (Talpidae) in the defunct order Insectivora on the basis of such close similarity as burrowing machines: forepaws modified as spades; atrophied eyes (superfluous underground) and no visible ears. Then there's the marsupial mole: Wikipedia says they are so similar to golden moles that they were once thought to be related despite the marsupial/placental divide. Of course, all three are now classified quite separately; molecular analysis has in fact torn down the whole disputed Insectivora order altogether.
Interesting to note convergent evolution depicted as a criticism of Stephen Jay Gould. One of Gould's consistent themes was the contingent nature of evolution: how randomness played such a role that any slight re-alignment would have resulted in totally different outcomes.
I don't see these concepts as being entirely in opposition. Gould's theme plays out on a much larger tapestry than the micro-evolutionary outcomes. Convergence doesn't necessarily mean, for example, that had the K-T meteor not wiped out non-avian dinosaurs, reptilian humans would have evolved. In the absence of that meteor, dinosaurs could have remained successful in their niches for many millions more years given no other environmental pressures.
I suspect that certain paths are available only for species at a certain level of complexity; yet evolution is not specifically directional towards complexity (merely towards variation in complexity)...
How convergence does and doesn't work, what it does do and what it doesn't, is a fascinating area of study.
Reference
Dawkins, R (2004): The Ancestor's Tale. Phoenix, London.
Sunday, February 24, 2008
Thingodonta: a salient lesson in analysis
So much to do, so little time. I would do more on non-paleontological subjects, but they keep getting crowded out...
New Zealand's SB mammal fossil has been interpreted as more archaic than therians (marsupials and 'placentals', referred here as metatherians and eutherians), although on a relatively similar par with monotremes, Australia's earliest known mammals and the world's most ancient extant lineage.
Mike Archer (et al)'s book Australia's Lost World includes a relevant anecdote about mammal classification.
The mammal is now called Yalkaparadonta, but started out as Thingodonta, because the teeth, uncovered first, were unlike any known clades of mammals.
A few months later, a jawbone turned up. It demonstrated three molars, where all plesiomorphic (both primitive and derived) metatherians had four [apart from some specialised groups] but eutherians properly had only three. Further, dental action was much more akin to that of eutherians, ie this would be the first early 'placental' in Australia.
New Zealand's SB mammal fossil has been interpreted as more archaic than therians (marsupials and 'placentals', referred here as metatherians and eutherians), although on a relatively similar par with monotremes, Australia's earliest known mammals and the world's most ancient extant lineage.
Mike Archer (et al)'s book Australia's Lost World includes a relevant anecdote about mammal classification.
The mammal is now called Yalkaparadonta, but started out as Thingodonta, because the teeth, uncovered first, were unlike any known clades of mammals.
A few months later, a jawbone turned up. It demonstrated three molars, where all plesiomorphic (both primitive and derived) metatherians had four [apart from some specialised groups] but eutherians properly had only three. Further, dental action was much more akin to that of eutherians, ie this would be the first early 'placental' in Australia.
In the third step, a skull turned up. Evidence now suggested it was a metatherian albeit quite primitive, and with a front section unlike any other.
Classification had switched back and forward; fortunately publication hadn't happened until the fuller story had emerged.
This creature isn't even listed on Paleos, although there's an entry at the Australian Museum site Australia's Lost Kingdoms and Wikipedia has some good (sourced but broken-linked) discussion on the classification difficulties. That discussion ultimately placed it in its own order, with some dissent from one Frederick Szalay who placed it as a (primitive) diprotodontan metatherian.
Some distinctiveness, some alignment with metatherians and with eutherian insectivores, with a good dose of convergent evolution thrown in.
Ah, convergence. Must be the bane of a taxonomist's life. But the lesson is that classification can be disrupted by hitherto unseen characteristics. For example, in the SB mammal, the femur suggests an abducted, or sprawling gait, although not as much so as monotremes. Yet that abduction must help place it, as it is placed, close to monotremes.
One must easily accept that the paper on the mammal brings together all current knowledge - at the time of publication. Yet it's understandable if there's much keenness to uncover more evidence, as a femur and two jaw fragments tell a tantalisingly curtailed story.
Reference
Archer M, Hand S J, Godthelp H (1991): Australia's Lost World: Riversleigh, World Heritage Site. Reed, Sydney.
Monday, February 18, 2008
Mammals 3: mammaliformes
Again: What is a mammal?
Of course, it's hard to draw the line. Any line is arbitrary, and doesn't reflect the incremental nature of evolution.
Taxonomists must be particularly grateful that the fossil record is gappy. The result is more harmonious: the appearance that ancestor and descendant species are somehow separate, whereas each evolutionary lineage is best represented as a continuum.
There are a number of characteristics that go towards making an animal distinctly mammal. The "canonical" signs include:
- the movement of the articular and quadrate bones from the jaw to the ear (as anvil and hammer)
- hair
- secondary palate (which enables mammals to eat and breathe at the same time).
Colin Tudge reckons homiothermy is a defining characteristic. This allows mammals to simply burn heat to keep warm, and is seen as a particular evolutionary advantage.
In a previous post, I mentioned the definition that mammals are the common ancestors (and all descendents thereof) of monotremes, marsupials, and placentals.
Other relateds are thereby referred to as mammaliformes. However, this is quite arbitrary, as the line is drawn at those currently living. Egg-laying monotremes are thus admitted in somewhat anomalously. They are non-therian mammals.
The split between mammals and reptiles occurs from the amnoite level. Reptiles (and birds and dinosaurs) are sauropsids. The mammal line of descent from amniotes runs through synapsids (from the Carboniferous period) to therapsids (mid-Permian) to cynodonts (late Permian). Synapsids through to cynodonts have been at various times in the past referred to as "mammal-like reptiles".
From there, we have the mammaliformes. The oft-cited Paleos is a fairly authoritative web site, referenced in Wikipedia (amongst many others) and with copious primary references (Paleos itself is being slowly expanded as a wiki here). The journey from cynodonts to mammals is detailed here.
Only trouble is, it's not quite in harmony with the paper on New Zealand's SB mammal (aka "waddling mouse"). The paper describes them as "more derived than morganuconodonts, and more primitive than multituberculates". However, the cladogram in the paper differs from that in Paleos. Both quote a nearly-identical set of sources, one of the main of which is a Chinese paleonotologist called Zhe-Xi Lou, who has done extensive work on early mammalian taxonomy.
More to come.
Of course, it's hard to draw the line. Any line is arbitrary, and doesn't reflect the incremental nature of evolution.
Taxonomists must be particularly grateful that the fossil record is gappy. The result is more harmonious: the appearance that ancestor and descendant species are somehow separate, whereas each evolutionary lineage is best represented as a continuum.
There are a number of characteristics that go towards making an animal distinctly mammal. The "canonical" signs include:
- the movement of the articular and quadrate bones from the jaw to the ear (as anvil and hammer)
- hair
- secondary palate (which enables mammals to eat and breathe at the same time).
Colin Tudge reckons homiothermy is a defining characteristic. This allows mammals to simply burn heat to keep warm, and is seen as a particular evolutionary advantage.
In a previous post, I mentioned the definition that mammals are the common ancestors (and all descendents thereof) of monotremes, marsupials, and placentals.
Other relateds are thereby referred to as mammaliformes. However, this is quite arbitrary, as the line is drawn at those currently living. Egg-laying monotremes are thus admitted in somewhat anomalously. They are non-therian mammals.
The split between mammals and reptiles occurs from the amnoite level. Reptiles (and birds and dinosaurs) are sauropsids. The mammal line of descent from amniotes runs through synapsids (from the Carboniferous period) to therapsids (mid-Permian) to cynodonts (late Permian). Synapsids through to cynodonts have been at various times in the past referred to as "mammal-like reptiles".
From there, we have the mammaliformes. The oft-cited Paleos is a fairly authoritative web site, referenced in Wikipedia (amongst many others) and with copious primary references (Paleos itself is being slowly expanded as a wiki here). The journey from cynodonts to mammals is detailed here.
Only trouble is, it's not quite in harmony with the paper on New Zealand's SB mammal (aka "waddling mouse"). The paper describes them as "more derived than morganuconodonts, and more primitive than multituberculates". However, the cladogram in the paper differs from that in Paleos. Both quote a nearly-identical set of sources, one of the main of which is a Chinese paleonotologist called Zhe-Xi Lou, who has done extensive work on early mammalian taxonomy.
More to come.
Monday, February 04, 2008
Evolution: basic mammal classification
As Australians will know more than most other people, there are three rather different types of mammals living today: (so-called) placentals, marsupials (kangaroos, koalas, etc) and monotremes (only the platypus and echidna). Whereas placentals predominate everywhere else, marsupials do so amongst the native Australian fauna, and the living monotremes are exclusive to Australia.
When it comes to classifying them, you can only go so far before losing scientific consensus. Traditional classification (taxonomy) is being superseded by cladistic taxonomy, where groupings are based on ancestor-plus-all-decendant clades. This outcome is most pleasing to someone like myself, valuing as I do the logic and neatness that it brings. Yet it also breeds confusion, rethinks, and re-classifications – very much so in the past decade or two, where molecular analysis tends to reveal true relationships, and shows that intuitive morphology (physical attributes) can be misleading, because of convergent or parallel evolution. Reptiles, for example, should no longer be referred to as a specific taxon, more a description – since mammals arose from their midst. They’re now often referred to as Reptilia*, with the asterisk to signify that status.
When it comes to classifying them, you can only go so far before losing scientific consensus. Traditional classification (taxonomy) is being superseded by cladistic taxonomy, where groupings are based on ancestor-plus-all-decendant clades. This outcome is most pleasing to someone like myself, valuing as I do the logic and neatness that it brings. Yet it also breeds confusion, rethinks, and re-classifications – very much so in the past decade or two, where molecular analysis tends to reveal true relationships, and shows that intuitive morphology (physical attributes) can be misleading, because of convergent or parallel evolution. Reptiles, for example, should no longer be referred to as a specific taxon, more a description – since mammals arose from their midst. They’re now often referred to as Reptilia*, with the asterisk to signify that status.
Three significant features of mammals are that the have fur (in general), give birth to their young life (in general), and they’re endothermic – that is, temperature regulation by internal means, eg the fur. (Terminology such as warm- or cold- blooded is not really sufficiently precise.) A key diagnostic can be taken as the movement of a couple of small bones in the jaw to become the hammer and anvil of the ear.
Current classifications of mammals is less solid than, say, Wikipedia would have you believe. If you look at their talk pages on the matter, you’ll see disagreement; their consensus emerges from a very small number of votes (see this one, for example).
For the moment, I’m going with Colin Tudge. He offers logic and a full narrative, which you can’t guarantee from Wikipedia. He frequently cites disagreement, and explains why his decisions fall where they do.
Following from this, mammals can be split into Theria (a sub-class) and non-therians. Theria is a sub-class of mammals that gives birth to their young live (rather than as eggs). They can be divided into infraclasses Eutheria (so-called placentals) and Metatheria (marsupials). It should be noted, though, that marsupials also give birth to live young – although at a rather less mature stage. Tudge in fact refers to this issue as a “movable feast” overall, when it comes to timing.
Next up: non-therians.
Reference
Tudge, Colin (2000): The Variety Of Life. Oxford University Press, New York.
Sunday, January 13, 2008
Evolution: In praise of cladistic taxonomy
I have been reading a wonderful book on taxonomy - with a cladistic approach - that positively elevates this discipline with its clarity, insight and interest.
It's The Variety Of Life, by Colin Tudge. Via a survey of all life - at the high level at least - it provides exactly the perspective on biological descent that I've always been looking for.
It starts at the highest level, kingdom, and chapter by chapter breaks down all life into taxonomical categories, based on evolutionary history - ie a cladistic approach.
In the normal approach to taxonomy, one can look at the topmost level of life and go on down. The general breakdown of life is:
Domain->Kingdom->Phylum->Class->Order->Family->Genus->Species
This gives a successive refinement of all animals, although there are sometimes sub- and super- levels interspersed to provide further refinement.
If you look at animals in particular, you would typically start at the phylum level. That is, dividing the animal kingdom by fundamentally different body types. There's about 32 animal phyla detailed here - although this number can vary widely depending on who's calling the shots, this seems to be a typical number.
Trouble is, most of those phyla are either small and insignificant, or marine. You'd wade through a lot to get to those that would have any meaning to most people on a day-to-day basis - that is, chordates (includes all animals with a backbone, which covers nearly all large animals), molluscs (covering shellfish and snails), and arthropods (mainly insects and crustaceans).
Unlike the typical simple listings of phyla given most places, where each phylum is accorded equal status in the headings at least, in a series of wonderful diagrams this book branches everything gradually from the top level, progressively dividing off the like from the unlike. In that sense, phyla with commonalities are grouped together, and branch off at the same time.
Cladistically speaking, there would be a term for just about every grouping, and these terms are well covered.
The narrative goes into detail about each successive breakdown, discussing all the biological similarities and differences. The book can be traversed as a map, with each chapter providing further diagrams in the cladistic breakdown, accompanied by a narrative that is thrilling in its clarity and enthusiasm.
Each diagram gives a pointer to following chapters that further breakdown the grouping under discussion. Although this navigation method could do with some improvements for those wanting to follow the maps - page references would help to lead from one diagram to both the following and preceding ones, and the full set would benefit by being reproduced in one hit at the beginning - these are minor distractions on what is, on the whole, a wonderful book.
The author is not dogmatic, and fully discusses differences of opinion on how the journey proceeds at each point, without disparaging those whose map would differ.
Thoroughly recommended as a reference book, or as one that can be read from beginning and end - albeit not it one sitting. There's too much life to cover.
Reference
Tudge, Colin (2000): The Variety Of Life. Oxford University Press, New York.
It's The Variety Of Life, by Colin Tudge. Via a survey of all life - at the high level at least - it provides exactly the perspective on biological descent that I've always been looking for.
It starts at the highest level, kingdom, and chapter by chapter breaks down all life into taxonomical categories, based on evolutionary history - ie a cladistic approach.
In the normal approach to taxonomy, one can look at the topmost level of life and go on down. The general breakdown of life is:
Domain->Kingdom->Phylum->Class->Order->Family->Genus->Species
This gives a successive refinement of all animals, although there are sometimes sub- and super- levels interspersed to provide further refinement.
If you look at animals in particular, you would typically start at the phylum level. That is, dividing the animal kingdom by fundamentally different body types. There's about 32 animal phyla detailed here - although this number can vary widely depending on who's calling the shots, this seems to be a typical number.
Trouble is, most of those phyla are either small and insignificant, or marine. You'd wade through a lot to get to those that would have any meaning to most people on a day-to-day basis - that is, chordates (includes all animals with a backbone, which covers nearly all large animals), molluscs (covering shellfish and snails), and arthropods (mainly insects and crustaceans).
Unlike the typical simple listings of phyla given most places, where each phylum is accorded equal status in the headings at least, in a series of wonderful diagrams this book branches everything gradually from the top level, progressively dividing off the like from the unlike. In that sense, phyla with commonalities are grouped together, and branch off at the same time.
Cladistically speaking, there would be a term for just about every grouping, and these terms are well covered.
The narrative goes into detail about each successive breakdown, discussing all the biological similarities and differences. The book can be traversed as a map, with each chapter providing further diagrams in the cladistic breakdown, accompanied by a narrative that is thrilling in its clarity and enthusiasm.
Each diagram gives a pointer to following chapters that further breakdown the grouping under discussion. Although this navigation method could do with some improvements for those wanting to follow the maps - page references would help to lead from one diagram to both the following and preceding ones, and the full set would benefit by being reproduced in one hit at the beginning - these are minor distractions on what is, on the whole, a wonderful book.
The author is not dogmatic, and fully discusses differences of opinion on how the journey proceeds at each point, without disparaging those whose map would differ.
Thoroughly recommended as a reference book, or as one that can be read from beginning and end - albeit not it one sitting. There's too much life to cover.
Reference
Tudge, Colin (2000): The Variety Of Life. Oxford University Press, New York.
Friday, January 11, 2008
Evolution: rivalry between the sciences
The advancement of evolutionary thought is most definitely a multidisciplinary affair. At its core, it requires an understanding of natural history (paleontology) and genetics - the macro and the micro, if you will.
They're all meant to be united in a detailed understanding of biology, but writings on the subject often betray the specialist's perspective on the other scientists involved in the quest for knowledge.
What I have read sometimes reveals the bias of the particular discipline. If I personally have a bias, it would be towards the sweeping overview of natural history. I find geneticists (such as John Maynard Smith and George C Williams), to paraphrase Mark Twain, all seem to talk about sex but not do anything about it. This apparently places me around the middle rung in the hierarchy.
I think it was Stephen Jay Gould who revealed that a traditional bias of paleontologists was that taxonomists (those essential scientists who analyse similarities and differences between species) are sometimes disparaged as being akin to stamp collectors.
John Maynard Smith in turn revealed that a traditional attitude to paleontologists had been to wish they would "go away and find another fossil, and stop bothering the grownups".
Smith bookended this with context. By way of introduction, he claimed that in the modern synthesis of evolutionary theory that emerged in the 1940s, paleontologists took part, but essentially only to confirm the facts uncovered by "the rest of us", and not to propose any new theory.
This at the beginning of an essay that ultimately praised paleontologists, and Gould in particular for advancing theory in recent times. Then again, Smith admitted to some surprise at the knowledge revealed in the narratives of paleontologists (ably assisted by geologists, climatologists and the like). Genetic analysis is relatively silent on major events such as mass extinctions.
Paleontology is often regarded as being insufficiently hard a science specifically because it often inclines to persuasive narratives, whereas geneticists would have you believe they own the realm of detailed analysis and logic.
Yet the geological and fossil records are thoroughly essential for an understanding of the origins, history and direction of life.
References
Maynard Smith, J (1984): Did Darwin Get It Right? Penguin, London.
Williams, G.C. 1996. Plan and Purpose in Nature. Weidenfeld & Nicolson, London.
They're all meant to be united in a detailed understanding of biology, but writings on the subject often betray the specialist's perspective on the other scientists involved in the quest for knowledge.
What I have read sometimes reveals the bias of the particular discipline. If I personally have a bias, it would be towards the sweeping overview of natural history. I find geneticists (such as John Maynard Smith and George C Williams), to paraphrase Mark Twain, all seem to talk about sex but not do anything about it. This apparently places me around the middle rung in the hierarchy.
I think it was Stephen Jay Gould who revealed that a traditional bias of paleontologists was that taxonomists (those essential scientists who analyse similarities and differences between species) are sometimes disparaged as being akin to stamp collectors.
John Maynard Smith in turn revealed that a traditional attitude to paleontologists had been to wish they would "go away and find another fossil, and stop bothering the grownups".
Smith bookended this with context. By way of introduction, he claimed that in the modern synthesis of evolutionary theory that emerged in the 1940s, paleontologists took part, but essentially only to confirm the facts uncovered by "the rest of us", and not to propose any new theory.
This at the beginning of an essay that ultimately praised paleontologists, and Gould in particular for advancing theory in recent times. Then again, Smith admitted to some surprise at the knowledge revealed in the narratives of paleontologists (ably assisted by geologists, climatologists and the like). Genetic analysis is relatively silent on major events such as mass extinctions.
Paleontology is often regarded as being insufficiently hard a science specifically because it often inclines to persuasive narratives, whereas geneticists would have you believe they own the realm of detailed analysis and logic.
Yet the geological and fossil records are thoroughly essential for an understanding of the origins, history and direction of life.
References
Maynard Smith, J (1984): Did Darwin Get It Right? Penguin, London.
Williams, G.C. 1996. Plan and Purpose in Nature. Weidenfeld & Nicolson, London.
Tuesday, September 04, 2007
Evolution, prehistory, and Bill Bryson
Had the opportunity to read through Bill Bryson's A Short History Of Everything. A book that attempts to be pretty much what it says, focused on natural history as opposed to human events.
I have to say, there's a lot of good stuff in it. Having said that, it's obviously written for the lay reader. Although loaded with facts, it's written in far too avuncular a style. Anecdotes can certainly be worthwhile, but often enough the writing is just one big ramble. The narrative is not particularly chronological, well-ordered, or of uniform significance.
Yet there's a lot to learn from it. I got flavours that I wouldn't have found elsewhere (especially not in reference works) in subjects such as biology taxonomy, human evolution, and climate change through time.
One strand running through the narratives is that biology and prehistory are not the clearcut, proven sciences that are presented in textbooks and references. I can see some justification for those publications sticking to a relatively unitary consensus position of scientists, rather than muddying the narrative with the labyrinthine internecine disagreements within a given discipline. It is to Bryson's credit that he's not afraid of muddy waters.
A few gleanings.
Taxonomy. There are seven major levels in biology: kingdom, phylum, class, order, family, genus, species. Humans, for example, are respectively animalia, chordata (vertebrates), mammalia, primate, hominid, homo, homo sapiens. Most animals are in a small number of the phyla; most phyla are completely obscure for the lay reader. But how many phyla to divide things into is a matter of dispute: from the twenties to the eighties, with most people settling on a number in the thirties. And as Bryson indicates, the divisions are made more rational every so often, with much grumbling and revision of textbooks. Books from the 1970s, for example, are most definitely out of date.
Climate change. There has been a lot of change through the course of this planet. (None before was anthropogenic, of course.) Bryson reckons there are reasons to argue both ways on whether the global climate could get hotter or cooler: the creation of the Himalayas and the central american isthmus had major impacts simply through changes in air and water flows. Consensus goes for the warming, but tinkering with the climate globally (as some have suggested) can have thoroughly wild results.
Human evolution. Theory is based on so few solid fossil records that the whole discipline could arguably be construed as risible. Even New Scientist frequently reports new developments with a straight face, while acknowledging each time that there are major disagreements on interpretation. NS's latest argument was on whether Homo Habilis and Homo Erectus overlapped - not at all? or for a few million years? The available examples are just so rare.
My take is that human evolution has been gradual, and the reason for the different species characterisations is simply because so few fossils have been found that they can easily be separated into different species. Heaven help us when we dig up much more, and find the changes too gradual for such distinction.
And finally, Bryson demonstrates that there is still so much to be discovered, named and catalogued, in both fossil and living species. If you're keen enough, you can almost certainly find (or at least differentiate enough) a new species that you can name after yourself. Better do so before extinction: humans are estimated to cause thousands of extinctions each year, many of them species still unnamed.
We are certainly not at the end of the history of science.
I have to say, there's a lot of good stuff in it. Having said that, it's obviously written for the lay reader. Although loaded with facts, it's written in far too avuncular a style. Anecdotes can certainly be worthwhile, but often enough the writing is just one big ramble. The narrative is not particularly chronological, well-ordered, or of uniform significance.
Yet there's a lot to learn from it. I got flavours that I wouldn't have found elsewhere (especially not in reference works) in subjects such as biology taxonomy, human evolution, and climate change through time.
One strand running through the narratives is that biology and prehistory are not the clearcut, proven sciences that are presented in textbooks and references. I can see some justification for those publications sticking to a relatively unitary consensus position of scientists, rather than muddying the narrative with the labyrinthine internecine disagreements within a given discipline. It is to Bryson's credit that he's not afraid of muddy waters.
A few gleanings.
Taxonomy. There are seven major levels in biology: kingdom, phylum, class, order, family, genus, species. Humans, for example, are respectively animalia, chordata (vertebrates), mammalia, primate, hominid, homo, homo sapiens. Most animals are in a small number of the phyla; most phyla are completely obscure for the lay reader. But how many phyla to divide things into is a matter of dispute: from the twenties to the eighties, with most people settling on a number in the thirties. And as Bryson indicates, the divisions are made more rational every so often, with much grumbling and revision of textbooks. Books from the 1970s, for example, are most definitely out of date.
Climate change. There has been a lot of change through the course of this planet. (None before was anthropogenic, of course.) Bryson reckons there are reasons to argue both ways on whether the global climate could get hotter or cooler: the creation of the Himalayas and the central american isthmus had major impacts simply through changes in air and water flows. Consensus goes for the warming, but tinkering with the climate globally (as some have suggested) can have thoroughly wild results.
Human evolution. Theory is based on so few solid fossil records that the whole discipline could arguably be construed as risible. Even New Scientist frequently reports new developments with a straight face, while acknowledging each time that there are major disagreements on interpretation. NS's latest argument was on whether Homo Habilis and Homo Erectus overlapped - not at all? or for a few million years? The available examples are just so rare.
My take is that human evolution has been gradual, and the reason for the different species characterisations is simply because so few fossils have been found that they can easily be separated into different species. Heaven help us when we dig up much more, and find the changes too gradual for such distinction.
And finally, Bryson demonstrates that there is still so much to be discovered, named and catalogued, in both fossil and living species. If you're keen enough, you can almost certainly find (or at least differentiate enough) a new species that you can name after yourself. Better do so before extinction: humans are estimated to cause thousands of extinctions each year, many of them species still unnamed.
We are certainly not at the end of the history of science.
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