Flightless Birds Don't Form a Natural Group

Last week I wrote about how paleontology provided an insight into evolution that genetic methods so far have not anticipated. I am not biased towards paleontology or any other field. It is futile to debate whether "my field is better than yours". Clearly evolutionary science benefits from a variety of inputs. More complimentary data the better.

Even so here I am writing about another finding where this time genetic methods produced results that fossils and morphological comparisons alone did not anticipate. Large flightless birds of the southern continents like the emu, ostrich, rheas and the kiwi were believed to be more closely related to each other than to other flighted birds. A genetic analysis has apparently redrawn the family tree of these birds.

It was thought that flightlessness evolved just once. I have depicted this scenario in the figure below.


Here flightlessness evolves in a stem or ancestral species. This happens when the southern continents are still part of the super continent Gondwanaland. The stem species gives rise to several descendant species. The flightlessness in each of these descendant species is a plesiomorphy or an ancestral trait inherited from the stem species. As Gondwanaland breaks up different flightless descendant species end up on different continents and diverge in response to the unique conditions.

But the recent genetic analysis indicates a different scenario. There may have been flightless bird species on Gondwanaland but none of them were the common ancestor of all modern southern continent flightless birds. Rather:


Loss of flight evolved several times on different continents independently in different lineages of flying birds. The flightless trait of the modern flightless birds is said to be an apomorphy or a derived trait in each of these lineages.

Why am I not that surprised? Here is what Edward Braun, one of the researchers had to say:

Scientists assumed that a single flightless common ancestor of the ratites lived on the supercontinent of Gondwana, which slowly broke up into Africa, South America, Australia and New Zealand; once divided, the ancestor species evolved slightly in each new location to produce the differences among the present-day ratites

So, the hypothesis that flightless birds formed a monophyletic group with respect to flying birds was never tested using morphological criteria? It seems that a convenient paleo-geographic story was available and so the assumption was made that flightless birds are monophyletic. Does this speak to the limitation of morphological comparisons for understanding evolutionary relationships or is there something else going on? Why was convergence i.e. the independent evolution of similar features never considered a possibility?

Off course the most heretical suggestion is that we still carry an unconscious bias for typological thinking, a tradition of grouping organisms that goes back well before evolutionary thinking. Flightless birds form a group or a type different from flying birds not because we know they are evolutionarily more closely related to each other but simply because they share the distinct trait of losing flight. No evolutionary scientist thinks this way any more.

Fishy Fingers And Why Paleontology Is Sooo Important

From my Science Daily Feed:

Tetrapods, the first four-legged land animals, are regarded as the first organisms that had fingers and toes. Now researchers at Uppsala University can show that this is wrong. Using medical x-rays, they found rudiments of fingers in the fins in fossil Panderichthys, the “transitional animal,” which indicates that rudimentary fingers developed considerably earlier than was previously thought.

Source: Uppsala University

Taxa ancestral to tetrapods had already evolved digits. They were re-sculpted and molded by evolution to serve new functions in tetrapods. So far nothing too surprising. As Francois Jacob had long observed, evolution is a tinkerer, adept at rejigging available parts to serve a different function.

But this is what caught my eye:

When they examined genes that are necessary for the evolution of fins in zebrafish (a ray-finned fish that is a distant relative of coelacanth fishes) and compared them with the gene that regulates the development of limbs in mice, researchers found that zebrafish lacked the genetic mechanisms that are necessary for the development of fingers. It was therefore concluded that fingers appeared for the first time in tetrapods.

Palaeontology gave us an insight on how evolution works that genetic techniques did not anticipate. Some time back Olivia Judson wrote an article on how the new fields of molecular genetics and evolutionary developmental biology are providing insights into the details of evolution that fossils cannot provide. I agreed with much of what she had to say. These methods are revealing the innards of the evolutionary process. But I don't agree that this somehow relegates paleontology to a bit player, a support role to the main actors in evolutionary science. This finding is a case in point.

I like to think of it this way. Let's say Mr. Bill Gates writes an article on how he became rich. But for reasons of whimsy he provides only a log showing the important financial benchmarks of his career. How much money he had in his account at various stages, some selected details of his stock holdings etc. Now, in a technical sense he has told us how he became rich, and from this log we can infer up to a point on the important events of his career. But we don't get a complete picture. The evolution of Mr. Gates from a college dropout to a very successful businessman took place in the context of a human ecology. Who were his childhood influences and his mentors? What did he learn from his interactions with his peers? How did the existing computer industry environment influence his decisions? All this makes for deeper insights and a more complete story of how he became rich.

Paleontology and fossils provide just such a broad ecological context to understanding evolution. When did a particular morphological trait arise? Just how did one morphological form get transformed through successive stages and how does this correlate to functional and ecologic shifts? At what rates did morphological features change? What long term patterns of morphological stasis or changes do particular lineages show? What was the nature of faunal turnovers at mass extinctions? What patterns of evolution do the survivor taxa show? Myriad such details that genetic techniques have little to say about and where paleontology is the primary source for understanding the history of life.

A Brief Return To Those Ancient Carbonates

I got an email from a faculty friend who teaches sedimentary geology and stratigraphy in the deep American south. Yes, they have Universities there too and daaawwg gon good ones I might add!

Can you summarize your thesis work and send it to me by this week? He's teaching a course in sedimentary petrology over this semester and needed some material for the carbonate part of it. I've spent this past weekend writing up a summary of my research on calcite cements of Middle and Late Ordovician basins of the southern Appalachians. Cements are chemical and biochemical precipitates that form between pore spaces of sediments and help bind loose sediment into rock. Their morphology and chemistry can tell a lot about ambient conditions of temperature, pore fluid chemistry and basin history. It's been several years since I thought and wrote about carbonates and diving into my thesis was fun. Here's a snippet:

Both the Middle Ordovician Chickamuga Group and the Upper Ordovician Shellmound Formation were affected by meteoric diagenesis relatively early in their individual burial histories. Detailed examination of the diagenetic products using petrography (light and cathodoluminescence ) and geochemistry (trace and stable isotopes) has shown that the precipitation environments were very different. Late Ordovician carbonates of southern Tennessee and northeast Georgia were exposed to subaerial diagenesis during Richmondian sea-level falls associated with the formation of the Taconic unconformity, and show substantial vadose and phreatic zone cements and alteration.

The underlying Middle Ordovician limestones also contain abundant phreatic calcite cement, but cementation is not related to synsedimentary emergence, or to direct vertical infiltration of meteoric water sourced from the overlying Upper Ordovician unconformities. Instead, recharging meteoric water in basin-margin highlands to the southeast, entered Middle Ordovician limestones through confined aquifers during Late Ordovician to Early Silurian times. This meteoric cementation history suggests that patterns of groundwater flow in the basin were strongly influenced by regional shale and lime-mud facies that occur between these two units. These low-permeability strata compartmentalized the Mid-Late Ordovician basin fill into contemporaneous, but hydrologically isolated surficial and deeper aquifers.

I wrote incredibly dense and cryptic passages such as these, not too confuse anyone. That's just the way formal communication in science sometimes reads like. My work was a comparative study of early diagenetic patterns in Middle and Late Ordovician carbonates. The climate changed from a Middle Ordovician greenhouse to a Late Ordovician ice-house and I wanted to find out if this left any impact on the diagenetic patterns.

In many ways I regard the 5 years of graduate research as the most creative period of my life so far. I struck a good rapport with my adviser early on, and a lot of positive outcomes flowed naturally from there. The informal graduate lab atmosphere made work enjoyable. And then there was the bonus of finding treasures like the one below.


I wrote in an earlier post on sea-level fall and the formation of erosional unconformities. The image shows a thin section of a limestone magnified under a microscope. This rock was sampled below a Late Ordovician unconformity. As sea-level fell and exposed the basin a fresh water aquifer developed in the sediments below the unconformity. Meteoric (fresh) water seeping down from the exposed erosional surface into the underlying sediment precipitated the early zoned cement in the pore spaces present between skeletal grains. These cements are tiny, rarely more than a millimeter along the long axis and can be seen only under a microscope. Much later in the Silurian the sea-level rose again and the Late Ordovician sediments were buried under a thick cover of Silurian sediments. The deep burial cement was precipitated then from fluids that were expelled from adjacent iron rich mud.

The image is taken in a cathodoluminesence microscope chamber. When you place a calcite sample in a vacuum chamber and bombard it with cathode rays, the sample will turn luminescent depending upon the presence of certain trace elements like Mn and Fe. The intensity of luminescence in calcite cements has been found to be related to the concentrations of Mn+2 and Fe+2, which act as activator and quencher of luminescence respectively. Reduction of Mn and Fe to a divalent state is necessary for these elements to enter the calcite lattice. In oxidizing pore-fluids, neither Mn+4 or Fe+3 is incorporated into growing calcite crystals, and thus cements are black (non-luminescent). In pore fluids with progressively lower Eh , reduction of Mn first and then Fe leads to their incorporation into the growing cements, giving the crystals a bright to dull luminescence.

That's what the black-golden-brown cement bands in the image show. An initial phase of oxidizing conditions in the aquifer that developed below the Late Ordovician unconformity. And then progressively reducing conditions as the Ordovician sediments got buried under Silurian age deposits.

I obsessed over such stuff for several years. I've moved on to other work which I enjoy as much. Well.... almost.

What do they say? The first cut is the deepest :)

Some Good Evolution Talks On NPR

I listen to Science Friday on Sunday. It's an old habit. I usually keep aside an hour or so, select what I want to listen to and then make some hot chai in preparation. Not the insipid hot water you get at overpriced coffee shops but real chai with milk, sugar and ginger. Then its podcast time. This week three good talks on evolution.

The first one was a short summary of a pretty important discovery. A gene sequence named HACNS1 that regulates gene activity most notably in the thumb, wrist and ankle. James Noonan one of the researchers explained that a comparison of this sequence with other species showed evidence of considerable evolution in the human version. They got the human version to express itself in genetically engineered mice and it triggered gene activity in the thumb and wrist area. The image below shows expression in the thumb of transgenic mice. The blue color is due to a reporter gene inserted along with HACNS1 to make it easier to identify areas where HACNS1 was being expressed.

Source: Yale Univ.

This may be one of the genes that gives dexterity to our forelimbs and digits. A natural question that came to me was when in our history did HACNS1 diverge from the ancestral version shared with early chimpanzees. I wish they had invited an anthropologist to give a fossil perspective. I dug around some literature and found out that early Australopethicines around 3.5 million years ago already had opposable thumbs different than chimpanzees and gorillas do. So looks like HACNS1 had diverged from the version inherited from the common ancestor with chimps by at least 3.5 to 4 million years ago. Maybe even much earlier if HACNS1 influences ankle development as well. Does it play a role in bipedality? The earliest bipedal hominids go back almost 6 million years.

The second talk was about the release of the new evolution game Spore. The game creator Will Wright along with beta tester evolutionary biologist Richard Prum discussed the game and what we can learn about evolution. Here's how a NYTimes report describes it:

The game begins with a meteorite crashing into a planet, sowing its oceans with life and organic matter. Players control a simple creature that gobbles up bits of debris. They can choose to eat other creatures or eat vegetation or both. As the creature eats and grows, it gains DNA points, which the player can use to add parts like tails for swimming or spikes for defense. Once the creature has gotten big and complex enough, it is ready for the transition to land.

And so on... The games focuses on adaptation and natural selection and so has been criticized for leaving out many other important mechanisms of evolution. No random genetic drift, no migrations and demographic shifts for example. Will Wright defended his approach, in effect saying that the intent was to get people interested in evolution. There are then many other formal avenues for detailed study . I agree with him. It's a game. Have fun. The problem is not that this one game doesn't represent evolution accurately, but that evolution is not covered adequately in school and even college level around the world. Fix that first.

And finally for those who like to unwind with a tall cool one. A talk on the biology and evolution of yeast that are used to ferment ales and lagers. Gavin Sherlock a geneticist from Stanford University discusses these life saving yeasts. Ale was around earlier. Then at some point, two ale yeast strains hybridized to form a new lager yeast. Hurray for the monk who supervised this momentous transition (did anyone else make beer in those days? :)) Lots more in this talk about beer and yeast.

Unfortunately I had had too much chai to switch to a frosty!

Can Strata Above An Unconformity Be Older Than Strata Below It

I just could not resist this. A paper on sequence stratigraphy in the August issue of Journal of Sedimentary Research by Nikki Strong and Chris Paola discuss just how such stratal relations can develop during the evolution of a passive margin lowstand systems tract. That is a lot of terminology. Passive margins are continental margins that form when plates rift and separate as result of sea-floor spreading. The east coast of the U.S and the west coast of India are passive margins.

These margins are characterized by quite a broad continental shelf. Large thicknesses of sediment accumulates on these shelves over time. These deposits are not one homogeneous body of sediment. Rather they are arranged in packages or bundles of sediment known as sequences. The controlling factor on the deposition of these sequences is the rise and fall of sea-level. Of interest here are fluctuations of sea-level spanning roughly 1-10 million years. These are known as 3rd order cycles and the sequences deposited within are called third order sequences. 2nd and 1st order cycles span larger time frames and 4th and 5th order span much smaller periods.

3rd order sequences have become something of a "working unit" for sequence stratigraphers. They are readily recognized in outcrop and in the subsurface using seismic profiling of basins. They also span a long enough period to record different phases of global sea-level history and basin development. Hence the focus on these sequences.

Several types of 3rd order sequences are recognized depending on what phase of a sea-level cycle they are deposited in. Each exhibit distinctive facies arrangements and stratal relationships (should I call it architecture? :)). Sequences deposited during a sea-level rise are called transgressive systems tracts. Those deposited when the sea-level rise has peaked are called highstand systems tracts. And those deposited during a sea-level fall are called lowstand systems tracts. The study of how these sequences evolve and how they are distributed in time and space is known as sequence stratigraphy.

Right. So as sea-level drops, it eventually exposes the continental shelf and an erosional surface develops. When sea-level rises again drowning the shelf, sediment will get deposited on this erosional surface. Geologists recognize this type of surface as an erosional unconformity. It is also a sequence boundary since it separates older sediment of the underlying lowstand systems tract from the subsequent transgressive systems tract. Knowing this how then can strata above an unconformity be older than strata below it?

It is something of a trick question since the researchers were not concerned with the subsequent transgressive systems tract but the complex evolution of the erosional unconformity. The researchers used an experimental basin at the Experimental Earthscape facility at the Univ. of Minnesota. The basin has a subsiding basin floor and a sediment supply system and these were manipulated to recreate scaled versions of lowstand systems tracts.

When I was doing graduate research in carbonates, modeling of sequences to simulate stratigraphic evolution of basins had gained recognition as a powerful tool which complimented outcrop and subsurface evaluation. Now you can get experimental data by recreating scale models of sequences.

That's cool!

The somewhat counter-intuitive stratal relationships develop because sea-level drop across the continental shelf is not instantaneous. The entire shelf is not exposed to erosion all at once or very rapidly. Instead as sea-level starts dropping, the shallower parts of the basin (think near the coast) are exposed early and an erosional surface develops on the exposed sea-floor. At this time the deeper parts (think shelf edge) are still below sea-level and may be active centers of delta formation.

Eventually on the exposed part of the shelf, i.e on the erosion surface a river valley may form and a fluvial depositional system may develop. Sediment is now accumulating on the erosion surface, while towards the shelf edge marine conditions prevail and deltaic sedimentation continues.

As sea-level continues to drop the erosion surface will get extended and keep overriding younger and younger deltaic sediments in shelf edge areas. But sea-level fall and the gradual exposure of the shelf has spanned so much time (often 100's of thousands of years) that often the very initial fluvial sediments deposited on top of the erosion surface will be older than the youngest deltaic sediments that have been recently overridden by the migrating erosion surface.

This may not come as something terrible new to geologists working in sequence stratigraphy but I thought the use of experimental data combined with a theoretical understanding of sequence development is a pretty powerful way to analyze basin evolution. Will this have any practical relevance when it comes to say correlating strata based on their position relative to a sequence boundary? I don't work in this field so I can't say how important such a result will be. But a work like this does remind us that those squiggly lines you see in a geological column and dismiss as just an unconformity, a time of no deposition, a hiatus when nothing but erosion took place, often have complex, protracted and interesting geologic histories of their own.