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

Sunday, October 25, 2015

Low Emissions Due To Ecofriendly Lifestyles? India's Climate Roadmap

India has submitted its Intended Nationally Determined Contribution to the United Nations Framework Convention on Climate Change. It is a sort of a road map the country will take with regards to future carbon emissions, mitigation and adaptation.

On page two I came across this gem:

Even now, when the per capita emissions of many developed countries vary between 7 to15 metric tonnes, the per capita emissions in India were only about 1.56 metric tonnes in 2010. This is because Indians believe in nature friendly lifestyle and practices rather than its exploitation.

What a load of bollocks!

Anyone familiar with the reality of life in India will recognize this as a specious attempt to explain away the low per capita emissions.

Emissions in India are low not because of nature friendly lifestyles but because of deep poverty. Hundreds of millions of people don't have access to enough energy... and the energy they are forced to exploit like burning cow dung, charcoal, wood and rubbish to sustain themselves is deeply injurious to their health.

On the other end of the spectrum, emissions from the increasingly affluent classes living mostly in cities are beginning to catch up with the developed world.

Nagraj Adve and Ashish Kothari critique the road map. It is not "nature friendly".

Tuesday, October 13, 2015

Open Access- History Of Life Articles In Current Biology

Update: November 6 2015- The articles are no longer open access.

This is a treat!

A special section in Current Biology on the History of Life with short essays and longer reviews on a variety of evolutionary history topics. So far I have read four:

The Cambrian Explosion - Derek E.G. Briggs
The Neoproterozoic- Nicholas J Butterfield
Novelty and Innovation in The History Of Life- Douglas H Irwin
Life in the Aftermath of Mass Extinctions- Pincelli Hull

These are densely written and immensely informative articles about various aspects of the evolution of the earth and its biosphere.

Couple of passages-

..from Novelty and Innovation in The History Of Life on the different styles of diversification seen in the fossil record-

Several challenges have arisen to claims that adaptive radiations are responsible for most evolutionary diversifications. For one, many events have been identified among both living and fossil clades that cannot be explained as the outcome of diversification from a single species. Examples range from the Cambrian explosion of animals, which involved many major clades but relatively few species, to the diversification of grasses. I have already discussed cascading radiations where increased diversity was driven by ecological interactions between clades. Other diversifications, for example the spread of a genus across a continent, may be largely non-adaptive. The most striking observation, however, is the absence of evolutionary novelty associated with classic adaptive radiations. Indeed, by their nature, adaptive radiations concern the adaptive exploitation of ecological opportunities via variation on existing adaptive themes, but not the formation of the themes themselves. While the fossil record documents adaptive radiations that encompass greater morphological diversity than Darwin’s finches, mockingbirds or Anolis lizards, including the spread of insects and angiosperms, and the Mesozoic radiation of mammals, the origins of morphological novelties often seem to involve a different process.

..from The Aftermath of Mass Extinctions-

Macroevolution is shaped as much by those who survive as those who did not [3,121]; it is shaped as much by extinction, as by innovation and speciation [3,122]. More than 99% of all the species that have ever lived are now extinct [3], and the losses have often been distinctly non-random [7,8]. The largest biotic crises eliminate entire branches of the tree of life [1], drive the decline of once diverse clades [123], and lead to the radiation of new species and ecosystems [13,124,125]. In the prolonged aftermath, ecosystem change across the globe exerts an evolutionary influence distinct from the extinction itself, with a timing characteristic of the earth system (i.e., earth system succession). As such, mass extinctions should not be considered as macroevolutionary point events, but rather as prolonged intervals of varying selection spanning the mass death and subsequent radiation of taxa.

The last line adds some perspective.... that although mass extinctions are defined by death, there is also evolution, often at elevated rates, going on during this interval. Groups of organisms which are able to adjust and evolve their way through environmental crises will find and occupy emptied ecologic niches and so to speak inherit a new earth to settle and diversify.

As you would have guessed from the articles I first dived into, my interest lies primarily on the broad patterns of evolution as revealed from the fossil record. But there are plenty more biology oriented articles to capture your interest. 

Current Biology

Sunday, October 11, 2015

The Social Utility Of Archaeology

Archaeologist Graeme Barker has been working on a Neanderthal site in the Kurdistan region in northern Iraq. In August 2014 he had to leave that region due to advances made by ISIS forces. Last month he returned to continue his studies.

He makes a pointed observation on the social uses of archaeology.

You have also worked in Libya through civil war and conflict. What has driven you to persist with these digs?

People say to me they won’t go on holiday where I choose to work next, but in both cases we embarked on the excavations in conditions of stability and then events took over! But these excavations are enormous intellectual opportunities. They are ways of tackling big, fundamental questions about the human past, using the techniques of modern archaeological science.

There is also a broader social purpose. Archaeology is often thought of as a cosy sort of subject, but most of the killing that is going on around the globe relates to people's sense of whether they are similar or different to each other, all of which is rooted in how they feel about their past and where they come from. Archaeology has a huge role to play in building civil societies that are comfortable with the complexity of their past.

This is very relevant to the situation in India too, where tension between ancient social divisions erupts into communal violence from time to time. 

Thursday, October 8, 2015

Groundwater Policy: Quis Custodiet Ipos Custodes

Who regulates the regulators?

In the context of groundwater policy, who will keep an independent check on government data collection methods and analysis which informs groundwater policy decisions.

It would be nice if government scientist themselves keep refining their methods, but equally needed are independent researchers from Universities and research institutions. Rahul Gokhale and Milind Sohoni of IIT Bombay analyze Maharashtra statewide groundwater data collected over the past few decades by the government Groundwater Surveys and Development Agency. The Agency in October of each year puts out a report on the groundwater outlook for the upcoming dry season (until June of the following year). This report relies on measured groundwater levels from ~ 5000 wells and the State rainfall data. However, there is substantial variation in groundwater levels throughout the dry season and between years in most wells.  By subjecting this data to statistical analysis and modelling study Gokhale and Sohoni conclude that aggregate rainfall data is a poor predictor of groundwater levels and that unmeasured factors like extraction patterns and land use influence groundwater availability. They point a way toward refining groundwater assessment methodology by incorporating local socio-economic and groundwater use data.

Now, on the face of it the finding seems somewhat banal, that groundwater levels and availability is controlled not just by rainfall patterns but other anthropogenic factors as well. However, it is important that someone dives into large government data sets and teases out these quantitative relationships between various interacting parameters. And it is good to see an Indian government agency share data willingly.


This paper looks at the crucial issue of dry-season groundwater-availability in the state of Maharashtra, India. We look at the two key hydro-climatological measurements which are used to implement groundwater policy in the state, viz., water levels in 5000+ observation wells across the state and aggregate rainfall data. We see that there is substantial variation in groundwater levels within and across the years in most wells. We argue that for a large number of these observation well locations, aggregate rainfall data is inadequate to model or to predict groundwater levels. For this, we use a novel random rainfall coefficient model for the purpose of modelling the effect of rainfall in a composite setting where extraction and changing land-use data is unknown. The observed high variance of this coefficient points to significant variations in groundwater levels, which may only be explained by unmeasured anthropogenic factors. Next, we see that the uncertainty in actual groundwater levels along with scarcity are two distinct features of groundwater availability and will elicit different behaviours from the typical user. Finally, we recommend that quantitative groundwater assessment protocols of the state should move to incorporating data from which extraction and land-use may be modelled. We believe this is one of the first studies where large spatio-temporal scale data gathered by state agencies have been analysed for scientific adequacy.

and a relevant finding and recommendation:

It is necessary to recognize that scarcity and uncertainty are mutually distinct features of a groundwater regime. For example, if groundwater was scarce but certain, the groundwater-user may make  a different set of socio-economic decisions as compared to when it were both scarce and uncertain. In the first case, it incentivizes efficient use of groundwater, while in the second case, it may well lead to competitive extraction and a race to the bottom, worsening the scarcity. Indeed, the spatial coincidence of large σα with σρ seems to suggest this. This leads us to the following policy recommendations: (i) recognition of scarcity and uncertainty as separate attributes of groundwater-availability and developing indices to measure uncertainty, (ii) further work into the incorporation of socioeconomic data along with hydrogeologic and climatic data for building groundwater assessment tools. Perhaps, one relevant avenue for this is the periodic water balance computation carried out by GSDA for each watershed, every 3–5 years (see GEC’97 1997). This incorporates considerable data on extraction, irrigation, surface water bodies, and estimates of other stocks and flows. A refinement of this water balance exercise may yield better inputs for the yearly outlook for the dry season.

Download paper here.