Wednesday, November 25, 2015

Agriculture Changed Us

.. and I don't mean just culturally,  but biologically as well.

Carl Zimmer in the New York Times summarizes recent results from a wide ranging study which incorporates the genetics of extant as well as ancient Europeans. The study found evidence for several instance of natural selection altering height, digestion, skin color and our immune system.

from the article:

Previous studies had suggested that Europeans became better able to digest milk once they began raising cattle. Dr. Reich and his colleagues confirmed that LCT, a gene that aids milk digestion, did experience intense natural selection, rapidly becoming more common in ancient Europeans. But it didn’t happen when farming began in Europe, as had been supposed. The earliest sign of this change, it turns out, dates back only 4,000 years.

While agriculture brought benefits like a new supply of protein in milk, it also created risks. Early European farmers who depended mainly on wheat and other crops risked getting low doses of important nutrients.

So a gene called SLC22A4 proved advantageous as soon as Europeans started to farm, Dr. Reich and his colleagues found. It encodes a protein on the surface of cells that draws in an amino acid called ergothioneine. Wheat and other crops have low levels of ergothioneine, and the new variant increases its absorption. That would have increased the chances of survival among the farmers who had the gene.

People who are followers of the going back to a hunter gatherer Paleolithic diet fad, take note. Our digestive arsenal and our micro-biomes have responded to a different agricultural food combination. Human evolution did not freeze with the coming of the ice age. Agriculture and animal  domestication have pushed evolution into changing our DNA.

For a more detailed treatment on human evolution over the Holocene, I recommend strongly Gregory Cochran and Henry Harpending's book - The 10,000 Year Explosion: How Civilization Accelerated Human Evolution.

Saturday, November 21, 2015

The Hobbit Evolved From Homo Erectus

That goblin of South East Asian forests continues to fascinate:


Homo floresiensis is an extinct, diminutive hominin species discovered in the Late Pleistocene deposits of Liang Bua cave, Flores, eastern Indonesia. The nature and evolutionary origins of H. floresiensis’ unique physical characters have been intensively debated. Based on extensive comparisons using linear metric analyses, crown contour analyses, and other trait-by-trait morphological comparisons, we report here that the dental remains from multiple individuals indicate that H. floresiensis had primitive canine-premolar and advanced molar morphologies, a combination of dental traits unknown in any other hominin species. The primitive aspects are comparable to H. erectus from the Early Pleistocene, whereas some of the molar morphologies are more progressive even compared to those of modern humans. This evidence contradicts the earlier claim of an entirely modern human-like dental morphology of H. floresiensis, while at the same time does not support the hypothesis that H. floresiensis originated from a much older H. habilis or Australopithecus-like small-brained hominin species currently unknown in the Asian fossil record. These results are however consistent with the alternative hypothesis that H. floresiensis derived from an earlier Asian Homo erectus population and experienced substantial body and brain size dwarfism in an isolated insular setting. The dentition of H. floresiensis is not a simple, scaled-down version of earlier hominins.

Open Access

Monday, November 16, 2015

Field Photos: Back Country Roads Of Deccan Volcanic Province

 These are the twin pinnacles of Tail Baila, a popular trekking spot near the Western Ghat escarpment about 100 km west of Pune. I get asked often whether Tail Baila is  a volcanic plug or a dyke. It is neither. The pinnacles  are lava  flows. There is a strong structural control over  erosion in  this part of the Deccan Volcanic Province. Take a look at the satellite imagery below.

I have marked in orange arrows, a strong roughly N-S oriented fracture system. In yellow arrows is a less prominent E-W oriented fracture system. The white dotted line is the Western Ghat Escarpment. These fracture systems have their origins in the tensional forces that broke apart fragments of Gondwanaland, with the Indian continental block separating from Madagascar around 88  mya and Seychelles breaking off from the Indian block about 66 mya. The latter rifting event coinciding with India drifting over a hot portion of the mantle known as the Reunion hotspot also triggered Deccan volcanism. Many of these fractures acted as conduits for magma to rise to the surface and spread as massive lava flows. Magma still occupies some of these fractures. These clogged up pipes are called dykes.

A paleo-geographic reconstruction of India in relation to other Gondwana continents and Asia during Deccan volcanism 66 million years ago is presented below.

Source: Sankar Chatterjee 2013

The legacy of these ancient tensional gashes didn't end with Deccan volcanism but has influenced the evolution of the landforms we see today. Since the lava pile is fractured, physical weathering -aided by water seepage, disruption by plant roots and by temperature changes- peels off slabs of lava along these weak fractures faces. Rock falls are a common site at the base of many cliffs. Removal of blocks of lava eventually results in the formation  of isolated mesas, buttes and pinnacles, remnants of once continuous lava flows. Streams follow narrow fracture zones and carve out steep sided canyons. The result, after eons of weathering and erosion, is a spectacular landscape with plateaus, narrow valleys,  high basalt cliffs  and pinnacles shaped as rectangular blocks like Tail Baila. 

Update- November 17 2015: Since this topic is of great local interest let me add another thought. The Western Ghat escarpment also has been undergoing this type of physical weathering and erosion along cracks and fractures. The original location of this escarpment would have been tens to a hundred km west of the present line. For millions of years the escarpment has been retreating eastwards as lava blocks have peeled off the cliff face. The Deccan Plateau was much wider in the past. It is being eaten up by eastward erosion. Places similar to Tiger's Leap and Konkan Kada would have been to the west earlier in geological time!

Last Sunday I drove with some friends on one of the loveliest back country roads in this part of the country. The interactive map below shows the route looping around the backwaters of  the Mulshi Dam from village Valane to village Nive.

A gnarly trunk  of the Peepal tree with the Mulshi backwaters

Thick lava flows of the Deccan Traps with crude columnar jointing.

In a distance a pretty colorful entrance to a temple is glimpsed through the trees.

 Serene backwaters

 A lonely stretch of road through a woodland...

 opens up with vistas of grasslands, upland forests and high basalt cliffs

Throughout the Holocene this tug of war has continued... where farmland meets forest.

  Distant pinnacles shimmer in the afternoon haze

When I was in college, geology was a road less traveled by. I am so glad I took it.

..until the next time.

Monday, November 9, 2015

Quote: Stephen Jay Gould On Paleontology

This study of periodicity of mass extinction was published last month-

Periodic impact cratering and extinction events over the last 260 million years - Michael Rampino and Ken Caldiera.
The claims of periodicity in impact cratering and biological extinction events are controversial. A newly revised record of dated impact craters has been analyzed for periodicity, and compared with the record of extinctions over the past 260 Myr. A digital circular spectral analysis of 37 crater ages (ranging in age from 15 to 254 Myr ago) yielded evidence for a significant 25.8 ± 0.6 Myr cycle. Using the same method, we found a significant 27.0 ± 0.7 Myr cycle in the dates of the eight recognized marine extinction events over the same period. The cycles detected in impacts and extinctions have a similar phase. The impact crater dataset shows 11 apparent peaks in the last 260 Myr, at least 5 of which correlate closely with significant extinction peaks. These results suggest that the hypothesis of periodic impacts and extinction events is still viable.

This idea is not new and I remembered Stephen Jay Gould's essay "The Cosmic Dance of Siva" (in The Flamingos's Smile) which describes one of the early such hypothesis followed by his trademark meditations of the role of paleontology in understanding the nature of evolution  and the history of life. Gould was always irked by the opinions held by many that paleontology is a dusty sort of a science, where people spend their careers fighting over species names, and that they have nothing important to say about the theoretical aspects of evolution. A large part of his popular science writing effort was devoted to demolishing  this notion. He was very successful in it with essay after essay beautifully demonstrating the utmost importance of paleontology in highlighting life's little oddities as well as its grand patterns.

Paleontology in the early 1970's underwent something of a change in attitude. Decades before "big  data" became a buzzword, researchers led by David Raup, Jack Sepkoski,  Leigh Van Valen and Tom Schopf, to name a few,  began amassing enormous data sets on fossil characteristics and species distributions and subjected them to rigorous statistical analysis in an effort to elucidate distribution of biodiversity and macro-evolutionary trends. Gould's own work was substantial. Ideas such as "punctuated equilibrium" (with Niles Eldridge) which relies on the fossil record to tease out patterns in the mode and tempo of evolution, were met with admiration as well as fierce criticism as was his thinking on the role of contingency and chance and the limits of natural selection and adaptive evolution as explanations for life's historical trajectories. His theoretical forays did make paleontologists think more broadly about their data and what it tells us about evolution but my take is that it didn't cause a revolution in evolutionary theory as was made out by the media and by Gould's  rhetoric. But he did elevate the status of paleontology and that can only be good for science.

He writes:

Most hot  ideas turn out to be  wrong. I can only hope that I will not be remembered as the man who campaigned with a name for the nonexistent (surely worse than a moon for the misbegotten). Some chances are certainly worth taking. If Thalia smiles and Siva exists, think what it all will mean for my beloved science of paleontology. We have labored so long under the onus of boredom and dullness. We are guardians of life's history, but we are often depicted as mindless philatelists of stone; specialists in tiny corners of space, time, and taxonomy; purveyors of such arcane names  as Pharkidonotus percarinatus in extended orgies of irrelevant detail. The editors of Britain's leading scientific journal wrote of us in 1969: "Scientists in general might be excused for assuming that most geologists are paleontologists and most paleontologists have staked out a square mile as their life's work." 

That impression has changed since to include paleontology as an important contributor to evolutionary theory. For that, the field owes him a debt.

Thursday, October 29, 2015

Fossils And The Origin And Diversification Of Birds
Stephen Brusatte and colleagues have a fine review article in Current Biology that brings together findings from the fossil record and molecular phylogeny work that throw light of the long history of bird evolution from Jurassic-Cretaceous to modern species.

Did you know .. that the remarkable Jehol Biota from northeastern China from 130  to 120 million years ago preserves thousands of bird fossils and accounts for nearly half of the global Mesozoic bird diversity? The Jehol Biota represents fossilization in wetland and lake sediments. The fine grained sediment size would have aided the superb preservation of these creatures. This fauna included small arborealists, semi-aquatic birds and large generalists but certain modern ecotypes like large aerial forages and aquatic specialists are not present. The End Cretaceous mass extinction produced empty ecologic niches for a greater diversity of bird forms to evolve.

..or that birds retain a single functional ovary and oviduct and a single oocycte is ovulated, shelled and laid per 24 hour cycle. Microstructural egg shell characteristics and small clutch size evolved incrementally in bird-like dinosaur ancestors who did retain two ovaries though. Earliest birds like Jeholornis and enantiornithines ( a basal group of birds) apparently had one ovary indicating that birds may have lost one ovary perhaps due to body lightening in response to the evolution of flight.

There is plenty of information in this essay on the long evolutionary history of bird like characters in dinosaur ancestors and the subsequent diversification of early (and now extinct) and post Cretaceous modern birds. It is not true that the end Cretaceous mass extinction affected only non-avian dinosaurs. Early birds had diversified into distinct groups by late Cretaceous and the mass extinction wiped out many of these lineages as well. Some lineages of the early birds (neornithines)did make it through the mass extinction. Molecular phylogeny indicates that all modern lineages formed within the first 15 million years after the extinction and then diversified quite rapidly and are today represented by 10,000 odd species.

But why write so much? The old adage " a picture is worth a thousand words" can be so true!

Just take a look at this lovely inforgraphic.

 Source: The Origin and Diversification of Birds

It summarizes the evolutionary relationship (phylogeny) of dinosaurs and birds and superimposes the evolution of traits that we recognize as typical of birds on a timeline from Triassic to the earliest birds (where Avialae/Aves branch out) . What we see is that these features evolved piecemeal over a 100 million year period in dinosaurs and some in the earliest birds, but not as a crazy spurt of morphological innovation that would have marked the geologically sudden appearance of a radically different creature.  Traits like bipedal posture, hollowed bones, wishbone, three fingered hands, wings and feathers, all appeared at successive stages in dinosaurs. Other traits like keeled breastbone to support flight muscles, endothermic metabolism and rapid growth, highly reduced tail, true muscle powered flight, and the loss of that one ovary, appeared in early bird lineages. The long story is that a lineage of therapod dinosaurs very gradually evolved bird-like characters so much so that experts find it difficult to separate bird-like dinosaurs from dinosaur-like birds.

Creationists smirk that experts can't even decide what is a bird and what is a dinosaur. Or that bird-like dinosaur fossils are younger than the earliest birds and so dinosaurs can't be the ancestors of birds. They are missing the point that the later appearance in the fossil record of bird-like dinosaurs is simply an artifact of preservation potential. This means that older bird-like dinosaurs haven't been found yet and that after birds branched out from dinosaurs the ancestral dinosaur lineage survived alongside birds. So, the sampled bird-like dinosaurs are not the direct ancestor species of birds but co-existing cousins. More importantly, the difficulty in taxonomic identification means that morphological transformations are being captured in the fossil record. This is strong evidence for evolution.

Meanwhile, just a thought from another paper I read recently on styles of diversification in the fossil record by Douglas Erwin. In the article he points out that the evolution of morphological novelty and spurts of diversification are often de-coupled  i.e.  novelty may arise in a species but that may not immediately result in an adaptive response in terms of exploitation of new resources and ecological space. Many novel traits that we recognize as typical of birds evolved much earlier in dinosaurs and it is not clear whether their evolution lead to an adaptive radiation in that dinosaur lineage. What did happen though is that at some point a threshold was crossed during maniraptoran (the closest relatives of birds) dinosaur evolution. We can think of  this as the dinosaur-bird transition. A collection of traits which had evolved piecemeal and under different evolutionary circumstances worked really well together and were co-opted and modified to serve different functions. The bird body plan then very successfully diversified into many different and new ecological roles.

Brusatte, S., O’Connor, J., & Jarvis, E. (2015). The Origin and Diversification of Birds Current Biology, 25 (19) DOI: 10.1016/j.cub.2015.08.003

Erwin, D. (2015). Novelty and Innovation in the History of Life Current Biology, 25 (19) DOI: 10.1016/j.cub.2015.08.019