Tuesday, September 29, 2015

Eukaryote Evolutionary Dynamics Through The Proterozoic


No, attention on evolution need not only be on dinosaurs, mammals and other large creatures. The Proterozoic, which is dominated by microscopic life also has a very interesting evolutionary story to tell.

Take a look  at this absolutely lovely info-graphic showing number and type of non-metazoan  eukaryote fossils in sampled stratigraphic units through the Proterozoic.

This was compiled by  Phoebe A. Cohen and Francis A. Macdonald from a literature survey of described fossil assemblages of non-metazoan Eukaryotes from Proterozoic stratigraphic sections from all over the world. The results show a dynamic living world in which biodiversity of eukaryotes fluctuated, tracking global ecological triggers. The bottom panel showing lithology in which fossils are found is important. You can see that mudstone (shale) dominates. Certain types of organisms favor certain types of sediment. Also, certain parts of organisms are better preserved in certain sediment types. This means that lithology can introduce a bias to the fossil record. There is plenty of sandstone in the Proterozoic. But soft bodied organisms don't get preserved too well in sandstone.  Carbonates are not very well represented too as host lithology in the fossil assemblages recorded. The Proterozoic has lots of limestone and dolostone sequences, but just like sandstone may not preserve soft bodied organisms as well as mudstones do. Proterozoic limestones generally have been found to contain the tougher recalcitrant fragments of eukaryote cells, so there is scope for carbonate sequences to be examined in more detail for their fossil content. Moving on, take a look at the distribution of phosphatic rocks. They appear in small time windows in the Tonian in early Neoproterozoic around 1000 million years ago and then much later in the Ediacaran beginning around 630 million years ago. Phosphatic minerals preserve fine details of soft tissue, but such type of preservation is restricted to only thin time slices.

Paleogeography may also bias the fossil record. Some locations may have accumulated the right types of sediments at the right time intervals. Location with respect to nutrient inputs and basin configuration may result in peculiar or endemic biota in that particular region. Add to that is a sampling bias. Deposits in some countries as just better studied resulting in a better fossil record. A journalist asked me recently why is the Vindhyan Basin in Central India so rich in fossils. This was in the context of the Proterozoic fossil record. The answer is that Vindhyans are not the exception. There is an improving fossil record from many Indian Proterozoic basins. A recent review by Mukund Sharma and colleagues summarizes this record...  I suspect though that the Vindhyan fossil record has been examined in a more systematic stratigraphic context so as to discern macro evolutionary trends.  An excellent paper by Purnima Srivastava  summarizes such evolutionary trends in the Proterozoic fossil record of the Vindhyans. She documents simpler prokaryote communities and moderately diversified megascopic unicellular eukaryotes in the early parts of the Proterozoic. In the Neoproterozoic she documents  more diverse and complex megascopic eukaryotes including the emergence of multicellular plant (bryophytes and sporophytes) and animal clades (Ediacaran fauna).

Source: Srivastava 2012

Explanation-  Megafossils from the Vindhyan Supergroup. (a) Association of Chuaria and Tawuia comparable with Jacutianema from the Rewa Group. (b) Dichotomous branching from the Samaria Shale, Bhander Group. (c) Association of Chuaria and Tawuia comparable with Jacutianema from the Rewa Group. (d) Carbonaceous disc with a cluster of small spheroids or a scale of some metazoan, Dholpura Shale, Bhander Group. (e) Carbonaceous vesicle with dinoflagellate-like features and two notches, Samaria Shale, Bhander Group. (f ) Chuaria-like carbonaceous discsarranged within a Tawuia-like elongated vesicle, Sirbu Shale, Bhander Group. (g) Close view of the hold fast-like  structure of (f ). (h) Chuaria with prominent and well-preserved inner body/nucleus and outer ring, Sirbu Shale, Bhander Group. (i) Carbonaceous ring, a part of the hold fast, according to the model proposed by Kumar (2001) for a multicellular plant from the Sirbu Shale, Bhander Group. ( j) Chuaria with spines/notches/ budding, Samaria Shale, Bhander Group. (k) Carbonaceous disc with two spines/processes, Samria Shale, Bhander Group. (l) Very thin filaments exhibiting branching, Rohtas Formation, Semri Group, Lower Vindhyans. (m) Small carbonaceous disc, with an umbrella-like protrusion (Sirbu Shale), comparable with the problematic microfossil Kakabekia from the Gunflint Chert (Barghoorn & Tyler 1965). (n) Very small-sized carbonaceous globules scattered haphazardly in an organic gel-like matrix, Sirbu Shale, Bhander Group. (o) Carbonaceous vesicles attached on a branched filament, Dholpura Shale, Bhander Group. (p) Branched filaments of the Dholpura Shale, Bhander Group.

Continuing a little more on the journalist's question about fossil record in India, there are other locations in the Himalayas (Krol Formation, Lesser Himalayas) and Rajasthan (Marwar Super Group) that also contain latest Neoproterozic sediments and offer rich scope for exploring the biodiversity of a very interesting period of earth history.

Coming back to the paper, the authors after taking lithological and geographic biases into account find a pattern of increasing assemblage diversity from the early Proterozoic up to the Cryogenic Period, which sees a fall in diversity. Cryogenic Period or " Snowball Earth" was a phase in the Proterozoic which saw episodes of widespread glaciations. Fossil assemblage diversity increases again in the Ediacaran Period.

Here is an extract from the paper that highlights the important questions about Proterozoic evolution that the authors address:

Here, we assess the existing record of Proterozoic fossils and test the robustness of this record by investigating potential biases presented by taphonomy, fossil categorizations, regional sampling, and uncertainties in age models. We then layer on existing paleogeographic, geochemical, and climatological datasets and assess potential relationships between eukaryotic diversification and environmental change. Questions we seek to illuminate with improved datasets include: What was the relationship between eukaryotic diversification and a putative rise in oxygen (Lenton et al. 2014; Planavsky et al. 2014)? Did the breakup of the supercontinent Rodinia lead to changes in the diversity and distribution of microfossil assemblages (Valentine andMoores 1970;Dalziel 1997; Hoffman 1998)? Was the diversification of crown group eukaryotes and origin of biomineralization (Parfrey et al. 2011, Cohen et al. 2011) driven by tectonically modulated changes in ocean chemistry (e.g., Halverson et al. 2010; Squire et al. 2006)? Did increased sinking of newly evolved mineralized tests drive changes in the biogeochemical cycles and climate (Tziperman et al. 2011)? What were the effects of global glaciation (a.k.a. Snowball Earth; Hoffman et al. 1998) on microeukaryotes? Were microeukaryotic diversification and the appearance of metazoans driven by predation (Porter 2011), changing ocean chemistry, or other factors?,

The connection with the breakup of  Rodinia is intriguing. Rifting of continents beginning around 830 mya and 780 mya lead to emplacement of large igneous provinces. Weathering of these silicate rocks resulted in an increased supply of iron and phosphorous to the oceans, leading to increase in primary productivity with effects down the food chain. Likewise, an increase in oxygen content in sea water may have provided many an impetus for the evolution of eukaryote complexity and diversity. Predation, a metabolically demanding activity may have been favored, as may an increase in cell size. Certain elements like Zinc which play physiologically critical roles in eukaryotes also may have been more accessible in the enhanced presence of oxygen.

Geological processes and biological evolution are intertwined and the Proterozoic fossil record provides ample instances of it. The origins of multicellular animals lie in the latest Neoproterozoic. The much later Cambrian "Explosion" which represents the geologically rapid diversification of the triploblastic biosphere grabs all the attention, but it is relevant to point out that a lot of the molecular machinery that animal cells rely on had already evolved in unicellular eukaryotes in various protist and fungal groups. Their diverse fossil record in the Proterozoic provides us with a broader understanding of the evolution of complexity.

Cohen, P., & Macdonald, F. (2015). The Proterozoic Record of Eukaryotes Paleobiology, 1-23 DOI: 10.1017/pab.2015.25

Friday, September 18, 2015

Harappa DNA- What Could It Tell Us About Holocene Peopling Of India

Hindustan Times carried a report a few days back on the recovery of DNA from Harappa age skeletons at Rakhigarhi village in Haryana.

What could ancient DNA tell us about the Holocene population composition of  India?


Recent genetic studies of  Indian populations  shows that Indians are a admixture of two ancient populations, the Ancestral South Indians (ASI) and  the Ancestral  North Indians (ANI). The general understanding is  that ASI has been resident  in India  since the Pleistocene, while ANI ancestry -which is related to Central and West Eurasians- was introduced in India  at various times during the Holocene. ANI and ASI are deeply divergent populations having separated from each other as early as 30 thousand to 40 thousand years ago.

ANI ancestry in Indian populations decreases along a north to south cline and from upper caste to lower caste.  Indo-European speakers have a larger component of  ANI ancestry than Dravidian speakers with North Indian upper castes showing the highest ANI ancestry.


Lets assume that a representative sample of Harappa society is eventually collected. What could Harappan DNA tell us?

1) There is an absence of ANI in Harappa DNA. Harappans are unmixed ASI. This would indicate that Harappans were not Vedic Aryans. It will also have implications on how farming was introduced to the Indus valley.

2) Harappans have some ANI ancestry i.e they are a mix of ANI and ASI . This would not automatically mean that the ANI ancestry was contributed by Vedic Aryans. ANI is likely a fairly diverse group i.e. different groups of ANI after separating from West Eurasians may have  migrated into South Asia at different times in the Holocene. There is a possibility that ANI ancestry in Harappans reflects the migration of farmers (Dravidian speakers?)  from West Eurasia in the earlier part of Holocene. Moorjani et al's study indicates waves of admixture of ANI and ASI,  with middle and upper castes showing multiple layers of ANI ancestry and northern Indo European language groups shows younger admixtures dates than southern Dravidian speaking groups. These have been dated to a late and post Harappan period, although the authors say that their methods may have missed earlier admixture events. I am predicting that any ANI component in Harappans will be taken by many people as confirmation that the Vedic Aryans built the Harappan civilization.

3) Harappans have some ANI ancestry with markers suggestive of Indo-Aryan people ; One example could be the proposed West Eurasian origin -13910 C>T mutation for lactase persistence which in India  shows a northwest to southeast declining pattern. This would favor the scenario that the Vedic Aryans were a part of the Harappan civilization.  And there could be other markers typical to Indo-Aryans. Needless to say, such a finding will upset linguistic reconstructions of Indo-Aryan origins (proto-Sanskrit) thought to be not earlier than 2000 B.C. 

4) Harappans are entirely ANI. This would mean that ANI co-existed alongside ASI in the Indian subcontinent but remained genetically distinct for thousands for years until admixture in late/post Harappan times.

We may get clear cut answers only when we can resolve with confidence the different layers of ANI ancestry.

I'm leaning towards Scenario (2). 

Wednesday, September 16, 2015

Coral Reefs, Atolls And Sea Level Rise

Will coral reefs and atolls (coral islands) be able to keep pace with the current and projected sea level rise and remain geologically stable in the coming decades and centuries? Will atolls in  the Pacific and Indian Oceans remain habitable?

Regarding  the first question,  I came  across a couple of recent  studies that suggest that reef growth in the Pacific, Indian and Caribbean seas has historically and in the geological  past been able to keep pace with sea level rise of magnitudes equal to or even greater than the current rate of change of sea level.

In a recent issue of  Geology, P.S Kench and colleagues study six time slices of shoreline position of the Funafuti Atoll in the tropical Pacific Ocean and find out that there has been no loss of  island due to erosion by sea level rise. This part of the Pacific has experienced some of the highest measured rates of  sea level rise amounting to about 5 mm per year over the past 60 years. Their analysis showed that reef islands in this group shifted their size, shape and positions in response to sea level rise.

What could be happening? Coral reefs are prolific producers of carbonate skeletal material. As sea level rises, corals grow upwards and outwards from established communities keeping pace with the sea level rise so as to remain in the optimum water depth range. Wave energy keeps breaking down corals and produce carbonate sand which then gets redistributed and deposited in adjacent areas including island beaches. Corals thus form a renewable supply of sediment that balances sediment lost to erosion. Thus coral islands, although may change in shape and position due to changes in depositional locus will not experience any net loss of land.

Studies which go back in geological time also seem to confirm that coral reefs have often extraordinary growth rates that they can sustain for centuries and may keep up with extremely rapid episodes of sea level rise. In a special issue of Sedimentology ( Feb 2015 Open Access) on carbonate response to sea level change, Gilbert F. Camoin and Jody M. Webster document very rapid coral growth rates  using age constrained fossil coral reefs from Barbados in the Caribbean Sea and from atolls in the Pacific and Indian Oceans.

Their results show that following the melting of the global ice caps beginning around twenty thousand years ago, coral reefs kept pace with high rates of sea level rise amounting to 6-10 mm per year and astonishingly in places like Tahiti, for periods of a few  centuries, amounting to 45 mm per year. This very high rate dated to 14.65 k to 14.3 k corresponds to a Melt Water Pulse i.e. an accelerated rise in sea level due to collapse of portions of the ice sheet. Healthy reef growth means a steady supply of sediment to replenish coral island beaches, thus maintaining geological stability through periods of sea level rise.

This suggests that many coral atolls will not simply vanish beneath the waves as sea level rise in the coming centuries, although they will change their shape and positions. The other danger besides sea level rise is the changing chemistry of sea water and other biological changes that might harm coral growth. Sea water acidification may slow down the capacity of corals to build calcium carbonate skeletons, although again, studies on the impact of changing pH on coral growth have shown mixed results, with ill effects on some coral species in some locations, while others seem to have sufficient internal buffering capacity to maintain normal growth patterns. Increasing sea water temperature may also result in a) expulsion of symbiotic algae that corals depend on, thus slowing down their growth and/or b) infection by parasites that might harm the coral animal. So, there is still much to worry about the health of coral ecosystems as the earth warms and ocean temperatures rise.

Now to the second question - will coral atolls remain habitable? Habitations on these islands are built on a foundation of dead coral communities and sand which are not going to be lifted up in response to sea level rise. Although the fringing living reef communities will supply sediment to these islands, powerful storms and high tides will still pose problems. Reefs don't form water tight sea walls around these atolls and tidal surges will bring sea water further inland.

Another problem is the impact of sea level rise on groundwater. Many of these island  communities rely on a thin fresh water aquifer for their water supply. The foundation of these islands is porous Pleistocene limestone. Holocene coral communities and sand is piled up on this Pleistocene foundation to build the island. The fresh water aquifer usually occurs in this Holocene sediment. The pores and fractures in the Pleistocene limestone below the fresh water lens is filled with sea water. The contact between the fresh water aquifer and the underlying sea water aquifer is called the Thurber Discontinuity. The graphic below shows a typical cross section and hydrogeology of a coral atoll.

 Source: Bailey et. al. 2010 adapted from Ayers, J.F.; Vacher, H.L. Hydrogeology of an atoll island: A conceptual model from detailed study of a Micronesian example. Ground Water 1986, 24, 2-15

What will be the impact of sea level rise on this fresh water lens. This is an active area of study and early results seem to suggest a variety of outcomes with small fresh water lenses further diminishing while larger ones persisting. This is a complex topic with a variety of controlling parameters like amount of eustatic sea level rise, island size and shape and island topography which will channel the extent of storm wave washover. As sea level rises over the next few decades and centuries, especially on coral atolls which are experiencing erosion and loss of land, the danger of salinization of the fresh water lens is a real possibility, which will make living on these islands a difficult proposition.

Tuesday, September 8, 2015

Understanding Global Warming- Consensus Via Committees

This is an important summary by Spencer Weart, historian emeritus at the American Institute of Physics, Maryland, on the growth of our understand of the risks posed by global warming. He does not point to any particular scientist or specific scientific papers that provided "breakthroughs" in our understanding of climate change and global warming. Instead, he says that the real actors were various committees set up to collate the diverse research done on climate change and to come up with a consensus on the risks climate change poses to humans.

A closer look, if I had much more space, would certainly turn up plenty of individuals, along with lots of mistakes and controversies about details. Each new idea was first brought up by someone and then argued out at length. Our history of committees is like the swan that glides serenely on the surface while paddling furiously underneath. Still, I haven’t been telling a Whig history, reconstructing after the fact an understanding that never existed at the time. In this peculiar case a consensus was constructed by committees on the fly, a consensus that became increasingly detailed and certain decade by decade. The topic was so important that people recognized very early on that it could not be left to a few individuals making statements to the newspapers. Experts had to analyze the entirety of the peer-reviewed literature, even have elaborate computer studies done expressly for their use, and get together to hammer out conclusions that everyone could agree were scientifically sound. To be sure, in some areas they could only agree on the extent of their uncertainty, but that, too, was a genuine and important scientific conclusion.

and this on public perception ..

I submit that a major problem in communicating climate realities to the public is that the media, and everyone else addressing the public, feature individual scientists and their discoveries and disagreements. We have scarcely come to grips with committee consensus, a different kind of history of science. You will find no account digging into details of committee deliberations. I haven’t been able to do it here, and I am not sanguine about prospects for getting it done. In fact, the IPCC and the NAS and their members have been highly reluctant to make public any documents or recollections about just what goes on in the committee deliberations. Only recently, under pressure from critics, has the IPCC made its review process entirely transparent to the public. Be that as it may, I suggest historians and social scientists should give more attention to those committees. If we did, the public would have a better idea of how “science” comes to say what it does say about global warming —and a good many other issues.

Read the article here..

HT @aboutgeology 

Tuesday, August 25, 2015

Theories Of Dispersal Of Homo Sapiens From Africa

Huw S. Groucutt and colleagues in Evolutionary Anthropology lay out the evolving story of the dispersal of Homo sapiens from Africa. The review brings together fossil, genetic  and archaeological data which now strongly leans towards a scenario of multiple migrations of Homo sapiens out of Africa beginning more  than hundred thousand years ago. These migrations followed ecological  windows of opportunity.  Interglacial phases resulted in wetter climate in the Levant and Arabia and may have made viable migration routes following either coastal contours or more interior passages towards the rest of Europe and Asia.

An Excerpt:

A variety of dispersal models (Table 1) address the period between the widely accepted African origin of Homo sapiens by around 200-150 ka and the arrival of our species at the margins of the Old World, including Australia, Siberia, and northwest Europe, by 50-40 ka.1–4 The evolutionary, demographic, and cultural processes between these milestones remain unclear, but a variety of recent studies add important new data.Whereas earlier models focused on assessing the geographical origins of our species based on fossil data, more recent approaches seek to combine fossil, genetic, archeological, and paleoenvironmental data to illuminate the nuances of dispersal into Asia (Table 1). These models emphasize different hypotheses concerning factors such as when dispersals began, how many occurred and which routes were followed. Recent models have largely fallen into two broad categories, emphasizing Marine Isotope  Stage (MIS) 5 (early onset dispersal model) or post-MIS 5 (late dispersal model) time frames (Table 1). This, however, is not a rigid dichotomy. For example, models proposing an early onset to dispersal are consistent with subsequent post-MIS 5 dispersals having also played an important role in patterns of human diversity.

The map below shows the distribution of Middle Paleolithic sites plotted on a modeled precipitation map of the last interglacial (MIS 5). The abundance of sites in the interior of Arabia speaks against a strictly coastal migration route into India. The interior of Arabia during humid phases would have been a mix of grasslands and riparian corridors offering potential dispersal routes into India and the rest of Asia.

Source: Huw S. Groucutt et. al. 2015

What is the Indian context?  The generally accepted earliest  modern Homo sapiens skeletal record in South Asia are ~35 k old fossils in Sri Lanka. But the tool record indicates presence of modern humans in India much before that. This review suggests that the totality of the tool records favors the theory that Homo sapiens may have entered India during MIS 5 more than a hundred thousand years ago, followed by additional  migrations beginning around fifty thousand years ago. Groucutt et. al. mention that future fossil discoveries from South Asia have the potential to transform ideas about the dispersal of Homo.

As of date the skeletal record of Homo in India consists of just a few fossils . Research by A.R.  Sankhyan and colleagues show that all of these have been found in the Narmada valley at Hathnora and a few km away at Netankheri . At Hathnora, hominin fossils occur in fluvial conglomerate and sand layer. One is a partially preserved calvarium and has been identified as a "robust" late Homo erectus or an archaic Homo sapien. Its cranial capacity is estimated to be 1200 cc to 1400 cc putting in the range of modern humans. It is associated with a collection of heavy duty large flake Acheulian hand axes and cleavers and chopping tools. The other fossil find at Hathnora consists of two clavicles and a partial 9th rib, interpreted to be belonging to a separate population of "short and stocky" archaic Homo sapiens associated with smaller Middle Paleolithic implements.  The cranium has been dated to the Middle Pleistocene ~ 250 k, while the clavicles and 9th rib appear to be younger with an estimated date to be ~150K range. A change in the ecology of this region is seen in the younger deposits based on the faunal content. The large flake tool industry disappears at this point in time . This has been interpreted to mean a migration of the larger robust archaic hominin away from this area based on appearance on this tool typology further north of this region and as far southeastwards to the Bastar region of Bihar.

At Netankheri, a partial femur and a humerus have been found. The femur occupies the same stratigraphic level as the Hathnora calvarium  and has been interpreted as belonging to late Homo erectus -archaic Homo sapien. The humerus though is of the "short and stocky" morphology and interpreted to represent an early modern Homo sapiens. Delicate bone implements have been found along with this fossil.  It is thought to be much younger, dated to be around 75 k, based on its stratigraphic position just below the Baneta Formation which contains Younger Toba Ash layers (ash deposits of the Toba eruption). The researchers interpret this to mean evolution from an archaic to a modern form, population continuity and continuous occupation of this area by this morphologically distinct hominin through the Middle and Late Pleistocene.

In summary, the skeletal and tool record points to presence of two culturally and physically distinct archaic hominin populations occupying the Narmada valley in the Middle Pleistocene. The tool record shows that Homo has been present in India for more than a million years and these physically distinct Middle Pleistocene hominins may be indicating the evolution of distinct hominin lineages in India. Or, was this population differentiation and morphological evolution inherited from an older African population structure, representing separate Middle Pleistocene migration episodes? And how they fit into the broader story of modern Homo sapiens dispersal and occupation of India remains to be worked out.

What is the margin of error on the 150 k date of the "short and stocky" hominin. Could they be younger and represent the early MIS 5 dispersal from Africa ( 100-125 K)?  Of interest are the ~35 K old Homo sapiens fossils from Sri Lanka which are physically distinct from the Netankheri "short and stocky" population. This points to another more recent (MIS 3) migration from Africa. Did these recent arrivals interbreed with the resident archaic hominins?  More fossils from South Asia are needed to fill in these gaps in our understanding of hominin evolution in India.  The authors of the Narmada hominins paper suggest that the "short and stocky" population may have contributed ancestry to later short bodied  populations of South Asia including the pygmies. Certainly, recent genetic work shows interbreeding between modern humans and other differentiated hominins like Neanderthals and Denisovans in Europe and East Asia respectively. Perhaps the Indian story is also one of assimilation of the earlier hominin populations with later human entrants.