Tuesday, October 18, 2016

Thursday, October 13, 2016

Sea Water Chemistry And Shell Mineralogy: Tales Of Mesozoic Bivalves

Years ago when I was in the second year of college, I along with friends, went for a fossil collection tour to the town of Ariyalur in South India. Rocks of Cretaceous age outcrop all around, and these strata have now become one of the most famous fossil localities in India.

We collected ammonites, echinoids, plant leaf impressions on clay and bivalves... lots and lots of bivalves.. In the picture below are the remains of my collection of molluscs. On the top left is an oyster with a clam clinging on to one of its valves. Bottom left is another oyster with its jagged valve margin. In the middle is a largish clam and to the right is an oyster whose layered shell structure is clearly visible.

I have some photomicrographs too taken from thin sections given to me by a friend.

In the above image the foliated shell microstructure of a piece of a bivalve can be clearly seen in cross polarized light.

And in the image below, a coarser prismatic crystal structure of a shell fragment is visible in the center of the image.

Most molluscs groups (including bivalves) in today's tropical seas built their skeletons using the CaCO3 polymorph aragonite. I say tropical seas, because molluscs with calcite skeletons are more common in temperate waters, such as for example in the marine communities living on the continental shelf of the southern coasts of Australia. In the Cretaceous seas though, even at tropical latitudes, calcite bivalves were common. In this apparent puzzle lies a very interesting story of climate change, sea floor spreading, changing sea water chemistry, the evolutionary decline and success of different bivalve groups during the Mesozoic, the emergence of bivalve reefs and the localization of hydrocarbon reservoirs.

Monday, October 3, 2016

Interview- Rosemary And Peter Grant On Watching Evolution In Action

Source: Quanta Magazine; Courtesy Peter and Rosemary Grant

Daphne Major in the Galapagos chain.

Yes, 40 years of field research on that half a square km size island, tracking, generation after generation, changes in body and beak size of different species of ground finches.  Lately, they have supplemented their morphologic and bird song data with genomic analysis to get an understanding of the genetic underpinnings of morphologic change.

Rosemary and Peter Grant interviewed about their epic evolution watch:

"The diminutive island wasn’t a particularly hospitable place for the Grants to spend their winters. At less than one-hundredth the size of Manhattan, Daphne resembles the tip of a volcano rising from the sea. Visitors must leap off the boat onto the edge of a steep ring of land that surrounds a central crater. The island’s vegetation is sparse. Herbs, cactus bushes and low trees provide food for finches — small, medium and large ground finches, as well as cactus finches — and other birds. The Grants brought with them all the food and water they would need and cooked meals in a shallow cave sheltered by a tarp from the baking sun. They camped on Daphne’s one tiny flat spot, barely larger than a picnic table.

...They visited Daphne for several months each year from 1973 to 2012, sometimes bringing their daughters. Over the course of their four-decade tenure, the couple tagged roughly 20,000 birds spanning at least eight generations. (The longest-lived bird on the Grants’ watch survived a whopping 17 years.) They tracked almost every mating and its offspring, creating large, multigenerational pedigrees for different finch species. They took blood samples and recorded the finches’ songs, which allowed them to track genetics and other factors long after the birds themselves died. They have confirmed some of Darwin’s most basic predictions and have earned a variety of prestigious science awards, including the Kyoto Prize in 2009".

indefatigable to the end..

"Do you plan to go back to Daphne?

RG: We stopped intensive work after 40 years, but we do plan to go back.

PG: The oldest person died at 122 years old. That means we have 40 more years".

Ground finches are off course the birds that Charles Darwin famously observed when on tour to the Galapagos, but infamously didn't mention in his book since he never labelled his samples according to their island location. He did borrow correctly labelled samples from other sailors and then had the ornithologist John Gould classify them. Gould's finding was that the islands finches were a group of sibling species despite their widely varying body and beak size and shape.

Habitats varied on different islands. Darwin realized that sometime in the distant past one ancestral population of finches must have immigrated from the South American mainland and then diverged into several morphologically distinct species, each a fit to its habitat. That was one of the threads of reasoning he weaved into a more comprehensive theory of common descent and evolution through natural selection.

The book, Beak of the Finch by Jonathan Weiner, is a bit dated but is still a riveting account of Rosemary and Peter Grant's research.

Update: @avinashtn alerted me to the Grant's book "40 Years of Evolution".

Saturday, September 24, 2016

No Population Continuity Between Pre Toba And Extant Humans In India

A few years ago stone tools were discovered in the Jurreru Valley region of Kurnool district, South India, in sediment stratigraphically below a volcanic ash layer dated to around seventy four thousand years ago. This was the deposit of the famous Toba eruption. Michael Petraglia, an archaeologist based at the University of Oxford, England, suggested that these tools were made by Homo sapiens. This would mean that our species had first migrated out of Africa and into India perhaps as early as hundred thousand years during the Marine Isotope Stage 5 interglacial phase when ecological corridors may have opened up between Africa, Arabia and the Indian subcontinent. This is much before the more commonly accepted dates of around fifty to sixty thousands years ago. Other scientists objected and argued that the tools were made by an earlier species of archaic Homo, perhaps descendants of Homo erectus who had migrated to India more than a million years ago. The various theories of the dispersal of Homo sapiens from Africa has been summarized well recently in an article by Huw. S Groucutt and colleagues.

The earliest unequivocal skeletal evidence of the presence of anatomically modern humans in the Indian subcontinent comes from Sri Lanka where these remains have been dated to be around thirty five thousand years old. They represent humans from the later wave of the out of Africa migrations.

A related question was left dangling. If these tools were made by people from an earlier migration of Homo sapiens, then is there population continuity between those older migrants and living Indians?  Did later migrants mix with the earlier inhabitants or did the earlier human populations go extinct without leaving a genetic legacy in us.

There were other hints of the presence of an older wave of Homo sapiens migration into India. The Indian Early to Mid Pleistocene hominin skeletal record is quite poor with examples only from the Narmada Valley at Hathnora and Nethankari . At the latter site, a humerus interpreted to represent a "short and stocky" early Homo sapiens has been found associated with delicate bone implements. The remains may be around seventy five thousand years old or even older. At Hathnora, two clavicles and a partial 9th rib was recovered from a layer of fluvial sediment. The materials are thought to be about one hundred and fifty thousand years old and have been interpreted to be an archaic Homo sapiens. What is the margin of error on these dates? Could they be a little younger and represent the early MIS 5 phase migration from Africa around one hundred to one hundred and twenty five thousand years ago? This population seems to have persisted for several tens of thousands of  years as is evidenced by the younger remains at Nethankari.

There is evidence in the form of tools  as well as skeletal material found in Israel, the Arabian Peninsula and China, that indicate that anatomically modern humans did migrate out of Africa as early as a hundred thousand years ago.  A series of DNA studies of global human populations published a few days ago seems to say that people from these earlier migrations died out without contributing ancestry to extant humans. The three studies say that all non-African humans have descended from a single wave of migration  that took place between fifty thousand and eighty thousand years ago.

The scientists, A.R. Sankhyan and colleagues, working on the remains of the short and stocky Narmada Valley hominin had suggested that this population may have contributed ancestry to later short bodied people of South Asia, for example the Andamanese tribes. This scenario now looks untenable. These older (putative) Homo sapiens  in India and elsewhere died out without leaving a genetic trace.

The exception to these findings seems to be in Papua New Guinea. One study finds that 2% of the genome of present day Papuans originated from an earlier expansion  of modern humans out of Africa.

Carl Zimmer has written a good summary of the results.

Here are the links to the papers -

1)  Genomic analyses inform on migration events during the peopling of Eurasia
2) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
3) A genomic history of Aboriginal Australia

Why didn't people from the two separate waves of modern human migrations mate? The answer likely is because they never met. These older Homo sapiens populations went extinct before the new settlers came. I say this because recent genetic work has shown that one almost inevitable outcome of the meeting of two peoples, however different they may be, is sexual intercourse. When modern humans left Africa fifty-sixty thousand years ago they met and interbreed with Neanderthals and Denisovans, two older hominin groups whose ancestors had left Africa about half a million years ago.

Consider also what happened much later in the Holocene. The end of last ice age and the advent of agriculture saw population growth and the migration and mixing of people. Many of these populations had diverged and remained relatively isolated for more than twenty thousand years, accumulating significant cultural, linguistic and physical difference between them. Yet, the result of the meeting of these people was mostly not the genetic disappearance of one group, but admixture and the formation of modern groups with multiple streams of ancestry.

Today's Europeans contain ancestry from three different groups. A small fraction from earlier resident hunter gatherers and the more substantial fraction from Near East farmers and from Central Asian steppe pastoralists. When Europeans began colonizing the Americas, the native populations suffered immensely from disease and subjugation. But there was also genetic admixture. Native Americans today, both from South and North Americas, contain a noticeable amount of  European and African ancestry.

In the Indian context multiple events of mixing in the Holocene took place between residents (the Ancestral South Indians) and migrants from the Eurasian regions (the Ancestral North Indians). Additions layers of ancestry to the Indian melting pot (but common more in the eastern parts of the country) were contributed by migration of the Tibeto-Burman and the Austroasiatic people from the north east.

Why did the older group of Homo sapiens go extinct? According to Dr Pagani, one of the scientists involved in the first study I listed above “They may have not been technologically advanced, living in small groups,”... “Maybe it was easy for a major later wave that was more successful to wipe them out.”

Or as I suggested, they went extinct before the new settlers arrived. Living in small isolated populations leaves people vulnerable to disease and environmental catastrophe. One such event could have been the Toba eruption which had considerable environmental impact in South Asia. Could that have played a role in the demise of older Homo sapiens groups in Asia?  It would be interesting to see if there is archaeological evidence of an overlap between the two groups of modern humans anywhere.

Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., Skoglund, P., Lazaridis, I., Sankararaman, S., Fu, Q., Rohland, N., Renaud, G., Erlich, Y., Willems, T., Gallo, C., Spence, J., Song, Y., Poletti, G., Balloux, F., van Driem, G., de Knijff, P., Romero, I., Jha, A., Behar, D., Bravi, C., Capelli, C., Hervig, T., Moreno-Estrada, A., Posukh, O., Balanovska, E., Balanovsky, O., Karachanak-Yankova, S., Sahakyan, H., Toncheva, D., Yepiskoposyan, L., Tyler-Smith, C., Xue, Y., Abdullah, M., Ruiz-Linares, A., Beall, C., Di Rienzo, A., Jeong, C., Starikovskaya, E., Metspalu, E., Parik, J., Villems, R., Henn, B., Hodoglugil, U., Mahley, R., Sajantila, A., Stamatoyannopoulos, G., Wee, J., Khusainova, R., Khusnutdinova, E., Litvinov, S., Ayodo, G., Comas, D., Hammer, M., Kivisild, T., Klitz, W., Winkler, C., Labuda, D., Bamshad, M., Jorde, L., Tishkoff, S., Watkins, W., Metspalu, M., Dryomov, S., Sukernik, R., Singh, L., Thangaraj, K., Pääbo, S., Kelso, J., Patterson, N., & Reich, D. (2016). The Simons Genome Diversity Project: 300 genomes from 142 diverse populations Nature DOI: 10.1038/nature18964

Groucutt, H., Petraglia, M., Bailey, G., Scerri, E., Parton, A., Clark-Balzan, L., Jennings, R., Lewis, L., Blinkhorn, J., Drake, N., Breeze, P., Inglis, R., Devès, M., Meredith-Williams, M., Boivin, N., Thomas, M., & Scally, A. (2015).               Rethinking the dispersal of
              out of Africa
             Evolutionary Anthropology: Issues, News, and Reviews, 24 (4), 149-164 DOI: 10.1002/evan.21455

Thursday, September 15, 2016

Photomicrograph- Ooid Growth Over A Foraminifera Nucleus

This week's microscopic view is from the Mississippian limestones exposed in the southern Appalachian mountains of Alabama.

Ooid cortices made up of tiny radial crystals of calcite growing around a foraminifera nucleus.

I will be putting up a longer post on ooids and oolite facies as important contributors of carbonate sand through geologic time and their significance as indicators of sea water chemistry and ecologic disruptions.

Stay tuned.