Tuesday, April 26, 2016

Maniraptoran Dinosaurs Show No Decline In Disparity Before Mass Extinction

Its hard to unravel and unpack complex phenomenon like patterns of faunal turnover during mass  extinctions. The methods chosen, the materials (fossils) available for study and the granularity of the study influences the results.

My last post was about a modeling study that concluded that for 40 million years before the mass extinction,  extinction rates exceeded the evolution of new species in many dinosaur lineages. Dinosaur diversity was declining towards the end of  the Cretaceous. Only a few herbivorous dinosaurs showed an increase in diversity.

Now a different study by Derek W. Larson, Caleb M. Brown , David C. Evans published in Current Biology focuses on just one sub group  of dinosaurs and comes to a different conclusion. This is an analysis of over 3000 teeth  of bird-like maniraptoran dinosaurs from 18 stratigraphic units in Western N. America which shows that there was no decline in disparity in different maniraptoran lineages for the last 18 million years before the mass extinction. The maniraptors were largely omnivorous but may have included specialized carnivorous and as well as herbivorous species.

Disparity is a measure of the range of variation of morphology, in this case teeth shape. This in turn is something of a proxy for the range of ecologic niches being exploited.

The authors remark-

Overall, these inferred ecomorphological patterns indicate that toothed maniraptorans, including toothed birds, were ecologically diverse and stable leading up to the end-Cretaceous mass extinction, at least in North America.

An interesting angle explored  in the paper is why toothed bird-like maniraptors and some lineages of toothed birds died out, while their physiologically and morphologically close relatives, the ancestors of modern birds, the Neornithes,  survived the mass extinction.

In the fallout of the bolide impact that marks the end of the Cretaceous, terrestrial food webs that relied on photosynthesis would have collapsed. However, seed banks derived from plants, including relatively abundant angiosperms, could have been a common, nutrient-rich resource that would have persisted among the detritus, which itself has been suggested as a key food source related to species survival across the boundary. With clearing of vegetation, either during a global firestorm or widespread burning of dead ground cover, exposed seeds in these areas worldwide could have been exploited by granivores. This pattern is observed in modern fire succession communities, where granivorous birds are the first avians to re-occupy disturbed habitats due to food resource accessibility. A persistent seed bank, which can remain viable for more than 50 years in modern temperate forests, most likely outlasted the catastrophic ecosystem collapse caused by a bolide impact and associated infrared thermal pulse, acid rain, darkness, and impact winter. Toothed maniraptorans, with their feeding systems adapted to faunivorous or potentially folivorous diets, would have been restricted to food chains dependent on living plant matter and unable to access these seed banks. Therefore, dietary specialization toward granivory in some lineages of crown group birds may have been one of the key factors in their survival through the end-Cretaceous mass extinction.

Although very similar to maniraptors, the Neornithes had evolved a unique dietary specialization. The presence of a beak, which served as a crushing apparatus, may have helped these ancestors of modern birds exploit seeds as a food source.

Tuesday, April 19, 2016

Decline In Dinosaur Diversity 40 Million Years Before Asteroid Impact

This is based on modeling of speciation and extinction rates.

Manabu Sakamotoa, Michael J. Benton,and Chris Vendittia

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

The paper is under a paywall so I won't comment on the details of the analysis. Ed Yong has written a good summary of the paper in The Atlantic.

I heard this research being covered on BBC News and out came the inevitable statement.. " dinosaurs may have been on their way out"... meaning even if there had been no asteroid impact the dinosaurs would have gone extinct soon. I am not  sure the researchers actually think this way. The dinosaurs were a very long lived group, originating in the Triassic about 230 million  years ago, with all the non-avian groups going  extinct 66 million years ago. In that time frame there were boom and  bust  phases. There were earlier episodes of rapid diversification , then decline and then recovery. The overall pattern seems to be a late Triassic to mid Jurassic phase of diversification, followed by a slowing down or small declines and small expansions of different groups thereafter.

Who knows, maybe the late Cretaceous decline would have given way to another period of recovery and diversification. Or, the branches of the dinosaur tree may have gotten pruned with many groups going extinct, but with some groups continuing to prosper. Dinosaurs were not one entity. They were a varied group.  The extinction of all non-avian dinosaurs 66 million years ago may create an illusion that their evolutionary fates were always co-dependent, but that need not be so. This analysis shows that even when many dinosaurs groups were declining in the late Cretaceous, a few herbivorous groups were diversifying.  All this came to an abrupt end because of the asteroid impact. Only the avian lineage of dinosaurs survived.

The one conclusion that can be definitely drawn from the dinosaur story is that random events and chance have played a huge role in shaping the history of life.

Tuesday, April 5, 2016

Peopling Of The Americas- Rapid Settlement And Substantial Lineage Extinction Upon European Contact

Here is the full paper : Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Several points of interest come to mind.

a) Separation with Siberian common ancestors took place about 24 thousand years ago, followed by a long period of isolation in Beringia (see Fig.).


The founder lineages then settled the America's quite rapidly beginning around 16 thousand years. Sites in Chile show human habitation by 14 thousand years.

b) The much talked about Clovis culture were not the first Americans.

c) There was a demographic collapse among the Native American populations. Charles Mann's 1491 gives quite a sweeping account of both native and Spanish eye witness accounts of the wiping out of entire tribes and communities due to Old World diseases. This paper backs that up using genetics. A comparison of ancient DNA with present day Native American DNA shows that extensive extinction of mitochondrial lineages took place.  In plain language, entire tribes were wiped out to be replaced  much later by natives migrating from some other place, although the authors caution some of the discontinuity of lineages could be because  modern diversity may have been undersampled.  The data for ancient DNA comes principally from the western coast of South America which had large Native American population centers.   Lowland populations went extinct more. Highland populations were less affected. Perhaps population contact was more in the lowlands and diseases like malaria more prevalent in the warmer climes?

Monday, April 4, 2016

What Is Speciation?

 Here is some evolutionary theory. Its a bit of a hard slog, but worth the effort.

Review article by Jessie Shapiro, Jean-Baptiste Leducq and James Mallet on "why speciation happens (or not) and the nature of the speciation process" -

Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation “in the act” and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent.

The included glossary does help.

Wednesday, March 23, 2016

In Search Of Early Humans In India

I attended a talk yesterday by Prof. S. N Rajguru on the evidence for early hominins in India. This was part of the C. Meenakshi Memorial Lecture series hosted by the Bhandarkar Oriental Research Institute in Pune.

Prof. Rajguru is an acknowledged expert on Quaternary geology and paleoclimates of the Indian subcontinent and the talk followed the contours of his expertise.

Here is the abstract which was given to us:

In Search of an "Early Man" (>2.5 Ma yrs to around 50 Ka yrs) in India

Recent progress in absolute dating methods, in understanding palaeo-landscape of India in light of behavior of monsoonal rainfall in the last 10 million years (Ma), fluctuations in sea level on 7500 km, long coastline of India and the rise of Himalayas and Tibetan plateau from 1000 m during the Late Miocene (around 15 Ma yrs ago) to around 3000 m during early Pleistocene(~1 Ma yrs ago) have added new information on chronology and environment of "Early Man" (hominin) in India.

It is now know that the Indian monsoon is at least 10 Ma old and was fairly strong till 2 Ma yrs. It started fluctuating (strong, moderate, weak) during the Pleistocene (2.5 Ma-10 Ka). The Indian monsoon was relatively strong to moderate during early Pleistocene (2.5 Ma - 0.7 Ma), moderate to weak during middle Pleistocene (0.7 Ma- 130 Ka) and weak during the late Pleistocene (130 Ka- 10 Ka).

Owing to changes in the strength of monsoonal rainfall the landscape of India also responded dramatically. The sea level went down by 100 to 150 m below the present sea level around 18 Ka BP (before present) and was high around 125 Ka BP by 5 to 7 m in tectonically stable part of coastal India. The peninsular rivers also responded to climatic changes in terms of strong erosion and excess deposition. The Himalaya was affected by tectonic movements and by glaical and interglacial climates which were part of global climatic changes during the Pleistocene.

These environmental changes did affect the biological world including 'hominins' in India.  It appears that early man was present in the foothills of the Himalayas in NW India around 2.6 Ma yrs BP and around 1.7 Ma BP in the coastal parts near Chennai in Tamil  Nadu. These two important discoveries in the form of stone tools and bones with cut marks made by early man raise doubts about the 'out of Africa' migration of early man in Asia during the early Pleistocene.

We are not certain who was the maker of stone tools like choppers around 2.6 Ma yrs or little  earlier in the foothills of the Himalayas near Chandigarh. Most likely he belongs to "Australopithicus" group of hominin. On the other hand 'Homo erectus' was responsible for making Acheulian (Lower Paleolithic) artifacts, like handaxes, cleavers, etc., around Chennai during the early Pleistocene (~ 1.7 Ma).

There is a long gap between 'Homo erectus' (~1.7 Ma, with brain capacity of 800 to 1100 cc) and modern man or Homo sapien sapiens (with brain capacity of 1100-1300cc) who had his origin in Africa 200,000 yrs BP.

In Indian context, there are large number of Lower Paleolithic sites well preserved in varieties of environment during the middle Pleistocene (0.7 Ma- 130 Ka). There is a cultural change in the form of stone tools consisting of small size scrapers, points, choppers, etc., made on flakes removed from cryptocrystalline minerals like chert and chalcedony. It is as yet not clear whether the maker of Middle Pleistocene artifacts was 'Modern Man' who arrived in India via West Asia, or he still belongs to advanced form of ' Homo erectus'. Excepting a single fossil skull of hominin, dated to around 250 Ka yrs in the Central Narmada Basin, we do not have any other human fossil data of early late Pleistocene (~ 100 Ka BP).  Thus, the search for early man, though shrouded in scientific controversy, will continue in future in old Himalayas, warm peninsula and in humid coastal strip of India.

A couple of quibbles. I'm sure he didn't mean it, but it sounds like changes in monsoonal strength led to a lowering of sea level around 20K- 18 K years ago. This is not true. The sea level dropped because sea water was locked in high latitude continental ice sheets during the Last Glacial Maximum.

Secondly is the comment that evidence of putative 2.6 million year old stone tools from the Siwalik foothills of the Himalaya raises doubt about the 'Out of Africa' migration of early humans into Asia in early Pleistocene. I really don't see how this is so. Unless you are claiming that bipedalism and hominins originated in Asia, a position for which there is not an iota of evidence, all this discovery does (and the finding is still being debated) is deepen the timeline of the earliest migration of hominins from Africa into Asia.

I came across the same argument in a more detailed article about the Siwalik stone tools and scratch marks on bovine bones discovery in Outlook magazine. That article went even further and stated that this 2.6 million year old tools and bone marking may tell us "when we started looking and behaving more like Homo sapiens rather than apes" Huh!... How so? How does an unconfirmed find of possible Early Pleistocene tools in India  signal the evolution  of Homo sapiens from ape like ancestors? The mere presence of these archaic tools can't be a signal. If so, the same reasoning applies to the Pleistocene tool record in Europe and China too. So, such a broad overreaching claim explains nothing.  It is just sensational journalism by Outlook magazine.

I don't want to dwell on this issue too much since it was not the thrust of Prof.  Rajguru's talk. Instead, he gave quite an engrossing presentation with lots of pictures of the various field sites where stone tools ranging in age from 1.7 million years to 50 thousand years or so have been found. He spoke in detail about the paleo-environments and it is clear that humans in India occupied a wide range of landscapes and ecology during the Pleistocene. There were some awesome sites in Ladakh in the Himalayas, a few sites along the Gujarat coast associated with mid-late Pleistocene aeolian carbonate sand made up of Miliolite shells (great cross bedding), and a very interesting site closer to Pune. This was in a laterite cave in a sea cliff overlooking the Arabian sea near the town of Guhaghar. Tools provisionally dated to about a hundred thousand years old or so have been found there.

What did come out of this talk was some of the limitations faced by researchers in India. The first is the lack of a skeletal record of humans. We have just a few skeletal fragments from the Narmada valley. I asked Prof. Rajguru about this lack of bones. He suggested that the African record is richer in bones because of preservation in volcanic ash and fine river muds and sands. In contrast, most of the sites where stone tools have been found in India are surface sites where the preservation potential of skeletal material is poor. That does point the way to a future program of more focused search for bones in the Pleistocene sediments across India. The second problem is establishing absolute chronology. Dating methods are very expensive and until recently Indian researchers could afford to date only the occasional sample. Or, they had to rely on collaboration with western (and Australian) researchers. Hopefully this will change in the future.

Prof. Rajguru is a field geologist. He must be in this seventies now but his enthusiasm for field work is still undiminished. He kept stressing the importance of understanding the geology, stratigraphy and paleo-ecology of human habitation sites to fully understand the significance and variability of human occupation in India in terms of past climates and landscapes. Even without skeletal material one can make a useful contribution toward understanding human evolution....

having said that.. we do need to find more bones!