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.