Category Archives: Paleontlontogy

Little Burrowers Are Important

The long history of the Earth includes periods of warming and cooling, including times with no ice and at least one “snowball Earth”, with ice covering the whole surface.  If nothing else, the geological record should teach us that in the long run, things can change a whole lot.

One of the interesting large scale events was the Cambrian explosion, a bloom of life 500 some million years ago.  At the time, the atmosphere was dominated by CO2 levels much higher than today, followed later by increased levels of Oxygen, presumably the byproduct of the spreading life. Some of the oldest lifeforms known were cyanobacteria which breath CO2 and emit O2 as waste.

These long term trends have reversed several times over hundreds of millions of years.  The levels of CO2 are, of course, linked to global temperatures.  But CO2 and other chemicals dramatically affect the chemistry of the oceans, which, in turn, favors different life forms depending on conditions.  (Today we are seeing a trend toward higher CO2, with concomitant effects on the oceans and global temperatures.)

The evolution of the atmosphere is no trivial matter of breathing out.  As we know today, chemicals from the atmosphere react with rocks and water, pulling constituents out of the air.  In the case of Oxygen, it reacts strongly with many elements, not least Iron, forming many oxides.  It also mixes with ocean waters, changing the acidity of the liquid and then reacting with yet other materials.

This summer a group of European researchers report a new analysis of yet another factor: the activities of sea bottom burrowers [1]. Today, these little critters have a surprisingly large role in the chemistry of the ocean and atmosphere. They only burrow a few centimeters, but this mixes up the sediments, letting in water, letting out chemicals, and generally causing a lot of biochemistry.

The new research pulls together many geochemical studies of the Earth’s past with a model of “burial, weathering and degassing processes, which transport chemical species between the atmosphere, oceans and sediments over geological timescales” (p. 4 ) The basic idea is to explore alternative scenarios with different assumptions about the amount and intensity of burrowing.

The fossil record indicates the evolution of ocean bottom burrows in the Cambrian period, with increasing evidence in the ensuing hundreds of millions of years. The research uses different assumptions about how active these diggers might have been, and then computes long term estimates of the global abundance of various chemicals.

The results suggest that even the early “moderate levels of shallow bioturbation have a large impact on sediment geochemistry”. (p. 8 ) Even the smallest entity can change the course of the future.

The authors also speculate that these animals may have a role in some of the complicated events in geological history.  As areas the ocean bottom became strongly anoxic, this could have led to extinction of burrowing species, which in turn dampened their effects, amplifying the climate change.

“There is a strong correlation between ocean anoxia, positive δ13Ccarb excursions and extinction events, and it is possible that the interactions between burrowing macrofauna, biogeochemical cycling and ocean anoxia may have contributed to these patterns.”

To paraphrase Lady Galadriel in the movie, ‘Even the smallest entity can change the course of the future.’

  1. Sebastiaan van de Velde, Benjamin J. W. Mills, Filip J. R. Meysman, Timothy M. Lenton, and Simon W. Poulton, Early Palaeozoic ocean anoxia and global warming driven by the evolution of shallow burrowing. Nature Communications, 9 (1):2554, 2018/07/02 2018.

Feathered Fossil Revises Family Tree of Birds

After the the Chicxulub impact there was a mass extinction, followed by a huge explosion of new species.  In recent decades we have learned more and more about these events, and as usually happens, the story gets more complicated the more we know.

One of the remarkable facts is how the great variety of not that different bird-like dinosaurs was sifted out, with only the modern-day birds surviving and spreading across the planet. What is the history and family tree of birds?  Where did different lines emerge, and how did they spread over the last 60 million years?

This summer, a new analysis of a fossil uncovered in Wyoming in 1982 found it to be a close relative of the ancestors of current day “banana eaters”, which live only in Africa [2].  The Wyoming fossil is reliably dated to 50 million years ago, so it looks like these birds lived in America at that time as well as Africa.  This group must have branched from other birds before that time, and spread from Africa to North America.  However they may have been distributed then, at some point, these birds died out everywhere except Africa.

nternational Turaco Society (From [1]_
This finding upends previous thinking about when and where this family of birds arose.  In large part this is because the study of living species focusses on the relatively abundant physical, geographical, and genetic data available, with little attention to the sparse and difficult fossil record of the ancestors of living animals.  These efforts derive putative family trees and evolutionary timelines even without reference to fossils.

The researchers point out that the new findings not only suggest a revised family tree, but offer “a valuable calibration point for neornithine molecular divergence dating analyses.”  There is nothing like a solidly documented specimen to constrain otherwise freewheeling data analytics!  The paper notes just how misleading results based solely on extant species can be, when compared to the same analysis with the fossil record included.

“[O[ur results serve as a cautionary warning against overreliance on extant data and high statistical support values when studying evolutionary processes that are fundamentally historical in nature.”


  1. Helen Briggs, Bird family tree shaken by discovery of feathered fossil, in BBC News – Science & Environment. 2018.
  2. Daniel J. Field and Allison Y. Hsiang, A North American stem turaco, and the complex biogeographic history of modern birds. BMC Evolutionary Biology, 18 (1):102, 2018/06/25 2018.

Dinosaur Dandruff?

Headline writers had fun with headlines like, Dinosaur dandruff reveals first evidence of skin shedding[1], but it’s a real find, and really important.

There has been much discussion about the outer covering of dinosaurs, which may have featured scales and/or feathers. But little is known about dinosaur skin, which is an integral part of this complex.

A new study reports on the analysis of fossils that contain flakes of skin from Cretaceous animals—essentially dinosaur dandruff [2]. <<link>> These fossils come from the wonderful fossil beds of North East China, which have yielded so many important views of the soft tissues of dinosaurs and early birds.

The remarkable fossils provide a rare view of dinosaur skin, “preserved with remarkable nanoscale fidelity”.  These samples reveal that these animals shed skin in small flakes, which reveal the cellular structure of the skin!  Who knew we could ever find such fossils?  Cool!

Skin and whatever covers it are, of course, a very import part of the thermoregulation of animals.  Consequently, these traces of skin tell us about the physiology of the animal.

First of all, shedding skin in small flakes itself is important. Reptiles shed in large molts, while birds shed small flakes continuously. This reflects continuous growth of birds, and suggests that these ancient birds and dinosaurs grew like birds, not snakes.

The skin also shows evidence of structures characteristic of modern feathered birds. This would indicate that avian skin and feathers co-evolved from early ancestors, before the development of flight.

However, the skin cells are distinctly different from modern birds. The structure is denser, with no fat, consistent with relatively little evaporative cooling compared to avians.  The researchers characterize this as “distinctly non- avian” and  indicating that “that feathered dinosaurs and early birds had a unique integumentary anatomy and physiology transitional between that of modern birds and non-feathered dinosaurs”.  This is consistent with the hypothesis that these ancient ancestors of birds had feathers but were not adapted for powered flight.

It’s really cool to find this kind of “missing link” for the physiology of the animals.  Who would have imagined we could actually find evidence that animals might have been “in between” the physiology of reptiles and birds?

But the coolest thing about this study was that they actually looked with their microscope!  Who would have thought that there could be intact, microscopic, fossil dandruff?  Who knows what other fossils may have similar micro scale remains that no one has looked for?  Get out your microscopes!

Very, very cool.

  1. Matt McGrath, Dinosaur dandruff reveals first evidence of skin shedding, in BBC News – Science & Environment. 2018.
  2. Maria E. McNamara, Fucheng Zhang, Stuart L. Kearns, Patrick J. Orr, André Toulouse, Tara Foley, David W. E. Hone, Chris S. Rogers, Michael J. Benton, Diane Johnson, Xing Xu, and Zhonghe Zhou, Fossilized skin reveals coevolution with feathers and metabolism in feathered dinosaurs and early birds. Nature Communications, 9 (1):2072, 2018/05/25 2018.

Roman Lead Pollution in Greenland Ice Cores

While it lasts, the ancient ice of Earth contains a record of the atmosphere, containing tiny bubbles of air, as well as whatever was in the air, including pollen and volcanic ash.  Ice also preserves traces of human activity, AKA pollution.

This spring an international team reports on a careful study of the chemistry of 423 meters of ice cores from Greenland, which they date to run from 1200 BCE to 1200 CE, some 2500 years [1].

The measurement found fluctuating traces of lead and copper apparently dating to historical times.  Given the location of Greenland, these metals presumably reflect emissions into the atmosphere from Europe.  The new study corroborate earlier isotopic analyses, showing that prevailing winds would transport emissions from ancient European activity to Greenland, while other putative sources would have little representation in Greenland ice. The study also compared the temporal patterns to lead traces in peat bogs, and found them to match.

The lead particulates are hypothesized to be from silver lead mining activity, in which high temperature smelting used lead as part of the process of recovering silver.  The process would have emitted lead into the air at major mining sites, such as Spain.  These would blow to Greenland, leaving a record of the mining activities in the ice.

While the record is variable and uncertain, there are periods of sustained high levels of lead in the record.  These were found to correllate with overall economic activity and presumably the intensity of mining.

The researchers report swings in mining that match recorded wars in Spain, which they argue reflects the disruption and intensification of silver mining due to political developments.

“The repeated pattern of dips in production coinciding with the outbreak of wars primarily affecting the Iberian Peninsula, and then recovery again after the end of each war, suggests that warfare caused major interruptions to lead–silver production during the middle and late Roman Republic.” (p. 2)

The sustained peace of Pax Romana is detectable in a long period of high lead levels in the Greenland ice, which ends at the time of a great plague.  This period probably reflects emissions from a number of sites in Northern Europe besides Spain. This peak drops off around 9CE, “coincident with Roman abandonment of territory to the east of the Rhine, including the Sauerland mines, after three legions were annihilated in the Teutoburg forest.” (p. 3)

The activity remained low until circa 800CE, a time when mining was intensified in medieval France and Britain. There is an earlier spike that is attributed to Phoenician activity, though there is no detailed record of mining in that period.

Finally, they find that these fluctuations in lead pollution tracked the metal content of Roman currency. Drops in the lead in Greenland correspond to periods of lower silver content in coins, presumably due to low production from silver mines.

“The fluctuations in lead–silver mining and smelting indicated by the Greenland lead pollution record and estimated lead emissions were directly reflected in the fineness and metallurgy of Rome’s silver coinage, the denarius…” (p. 3)

This is a pretty cool study, and the detailed dating of the records is pretty impressive.  Cross referencing peat bogs, volcanic activity, and historical records is a good idea, though I worry that the study is combining multiple imperfect measurements, hoping the combination is better rather than worse.

A key of the study is the simulation of the atmospheric deposition, and I worry that it is logically circular.  This kind of simulation is tricky under any circumstance, and projecting thousands of years into the past is problematic. The researchers are well aware of this, and are reasonably careful about how they use the simulations. They look at general circulation patterns, not short term events, projecting from the last century of detailed data reports.

There are two questions that nag me about though.  First, there is an assumption that the general circulation is basically unchanged over the last 3000 years. I’m not sure that is true, but it may well be true for the effects of interest in this study (i.e., wind blown particles transported from Europe to Greenland).  I simply don’t know. If there was a big enough change in wind patterns during the period, this could show up as a drop in lead that has nothing to do with mining activity.

The study makes a number of claims about the sensitivity of the Greenland ice record to sources in different geographical locations (Figure 1 in the paper).  Mostly, this is a matter of distance, which is straightforward.  But they also find some substantial differences in locations not that far apart (Spain versus Britain versus  Germany), from which they infer proportionate responsibility for the lead pollution.

Essentially, they work backward from the measured lead to various potential sources where ancient mining was known to have occurred. Granting these calculations are mainly correct, they are mainly looking at known sources from the historical and archaeological record. If there are other sources, they would be difficult to detect in this methodology, and they would be misestimating the contributions of the known sources. If there are other mines unaccounted for, the whole result could be way off.

Future work may be able to extract detailed isotope composition from the deposits, which might reveal the sources more directly. I fear that that will be difficult to achieve from these ice cores.

These simulations are aligned with known history, but that is (literally) post hoc reasoning. Basically, they are able to find explanatory events for major changes in the lead pollution, including at least one surprise (i.e., the outsized effects of the Antonine plague, among sever plagues and wars).  Yet there are plenty of other events that do not show up in the lead pollution record.  I would note that the history of the metallic content of Roman coins is complicated, and not necessarily tied to the production of silver as the key factor.

In short, the perceived correlation between the ice core records and historical events is self-confirming.  Who knows how many alternative events might be chosen that do not match the ice cores as well?

In any case, the study doesn’t actually reveal any new findings. It shows that ancient industrial activity may well be reflected in Greenland ice, and that pollution seems to be correlated with the overall mining activity in Europe and the Mediterranean (but not China or other more distant locals). In fact, it would be surprising if this were not true.

What the study does seem to prove is that methods have improved to be able to at least provide detailed support for this kind of historical hypothesis, even if it isn’t really able to confirm or deny detailed hypotheses.

  1. Joseph R. McConnell, Andrew I. Wilson, Andreas Stohl, Monica M. Arienzo, Nathan J. Chellman, Sabine Eckhardt, Elisabeth M. Thompson, A. Mark Pollard, and Jørgen Peder Steffensen, Lead pollution recorded in Greenland ice indicates European emissions tracked plagues, wars, and imperial expansion during antiquity. Proceedings of the National Academy of Sciences, 2018.

Reconstruction of an Ancient Bird’s Beak

One of the intriguing questions of evolutionary biology is just how birds emerged from other dinosaurs.  In recent years we have seen a flood of feathered dinosaurs and early birds, all from approximately the same time.

These animals are clearly related to each other and are ancestors of both contemporary birds and other lines of dinosaurs that died out.  In fact, the new evidence has made the picture even more complicated, because there seem to be anatomical and behavioral convergences in these species.  It’s more of a family bramble than a family tree.

In addition to the obvious questions about the origins of feathers and flight, there is a longstanding mystery of the bird’s beak. Most dinosaurs (and reptiles and mammals) have teeth, most birds don’t.  How (and why) did birds evolve beaks? How did they lose their teeth?

This question has only been complicated by fossil finds of early species that look like birds with teeth, as well as dinosaurs and other animals with beak-like mouths.  For that matter, beaks are part of a characteristic avian skull and brain case, which is quite different from skull of other animals.

Well preserved “missing links” have been, well, missing.

This summer researchers from several institutions report on a study of Ichthyornis dispar a toothed bird from the late Cretaceous [2]. The new work is based on an unusually well-preserved specimen recently found, plus other specimens from collections, including several “undescribed” fragments, i.e., specimens that have been gathering dust in some back room.  The skulls were CT scanned and the data combined to create a fairly complete 3D model of I. dispar cranium.

The reconstruction shows a considerable number of features that are clearly similar to birds.  The merest glance catches the beak and eyes of a bird.  The CT scans also reveal that the brain was extremely birdlike as well.  At the same time, I. dispar also had teeth and robust jaw muscles of other dinosaurs.

Figure 1 | Skull of the bird Ichthyornis dispar. Field et al.1 report the reconstruction of the skull of an extinct species. Their reconstruction fills in some structures missing from previously available fossils, thereby illuminating the transition between the loss of ancient dinosaur features and the evolution of characteristics found in present-day birds. The sections in yellow are newly identified fossil material, whereas the grey structures have been described previously. a, A side view of the skull. b, A view from above the skull (beak positioned on the left) showing cross-sections in two focal planes. The section above the black line is closer to the top of the skull than the region below the black line. Scale bar, 1 centimetre. (Adapted from Extended Data Fig. 2 of ref. 1.) (From [3])

In short, this species turns out to be a classic “missing link”, clearly suggesting the evolutionary history of the heads and beaks of birds was gradual and piecemeal.

This finding is particularly satisfying because Ichthyornis was discovered a long time ago, and has been subject to speculation about the connection between dinosaurs and birds since Darwin’s day [3]. The new reconstruction shows that this “missing link” was there from the very beginning!

Right under our noses this whole time was an amazing, transitional bird,” said Dr Bhart-Anjan Bhullar. (quoted in [1])

  1. Helen Briggs, How birds got their beaks – new fossil evidence, in BBC News – Science & Environment. 2018.
  2. Daniel J. Field, Michael Hanson, David Burnham, Laura E. Wilson, Kristopher Super, Dana Ehret, Jun A. Ebersole, and Bhart-Anjan S. Bhullar, Complete Ichthyornis skull illuminates mosaic assembly of the avian head. Nature, 557 (7703):96-100, 2018/05/01 2018.
  3. Kevin Padian, Evolutionary insights from an ancient bird. Nature, 557 (7703):36-37, 2018/05/01 2018.


Megafauna Extinction Linked To Human Ancestors

One of the glaring facts of human prehistory is the correlation of the rise of humans and the decline of megafauna—big game.  This pattern continues today, with simultaneously accelerating extinctions of large animals and booming human populations.

Many of us think this pattern is no coincidence.  We know that people will hunt anything and everything to extinction.  All those nasty little apes with their pointy sticks probably did in the giant sloths and other big beats.

Cautious souls reserve judgement, because it is certainly possible that some third factor, such as changing climate, led to both more humans and fewer game animals.  Just because we are killing everything in sight today doesn’t mean that humans wiped out ancient all the ancient fauna.

Given the sparse and uncertain data about exactly when and where humans lived, and when and where species went extinct, there is only circumstantial evidence one way or the other. Correlation is not causation.

So, what role did we humans and our cousins play in the large die off at the end of the Pleistocene?

This spring, a group of researchers published a study of mammalian extinctions and human expansion from the last 125,000 years [2].  The study worked with a dataset that includes mammalian body size distributions and biodiversity over time.

“We investigated the influence of these emerging and increasingly sophisticated hominin predators on continental and global mammalian biodiversity over the late Quaternary” ([2], p.310)

Of particular interest are five broad periods of time corresponding to the expansion of hominins (humans and cousins).

The analysis showed a clear relationship between size of the animals and likelihood of extinction, especially in the earlier periods.  This means that larger animals were consistently wiped out.  Notably, a similar analysis for periods before the Pleistocene (before homonins) do not show this pattern.  (The pattern is less visible in recent times, likely because everything is being wiped out at the same time.)

“As Neandertals, Denisovans, and humans spread across the globe over the late Quaternary, a highly size-biased extinc- tion followed, a pattern distinct in the Cenozoic mammal record. The subsequent downgrading of body size was severe and differentially targeted herbivores.”

This pattern is consistent with human hunting behavior, and is seen at the precise periods when humans were expanding.

One interesting conclusion from this data is that this pattern began very early, and, indeed, before Homo sapiens evolved from earlier Hominids.  This implies that our ancestors have been big game hunters from the beginning, and have been significantly impacting big game from forever.  (Nasty little apes with pointy sticks…)

This pattern has abated in recent ages because humans have come to dominate the Earth, and domesticated animals have replaced wild animals.  The study projects into the future, assuming that threatened species die out. In the future projections, the extinctions extend into smaller animals, indeed, nearly all wild mammals.

I was inspired to make my own plots from some of their data (I drew from Table S1, Supplemental materials).  These diagrams make plain the extremely rapid decline in animals with large body mass, and the key temporal pattern:  extinctions began very early in Africa and Eurasia, spread out to Australia and then the Americas.  This is, of course, the path of human occupation.

I drew arrows suggesting when humans arrived and expanded.  Note that these marks are impressionistic, dates and scales of human occupation are not well established.

(In these diagrams the last point is the projected future extinctions in then next 200 years, which is a precipitous drop.)

From [2] Supplemental Materials, Table S1. Horizontal axis is years (1000s), vertical axis is median body mass for surviving species. Lower median body mass means fewer large animals. Arrows suggest when major human infestations may have first occurred.

  1. Christopher Joyce, New Study Says Ancient Humans Hunted Big Mammals To Extinction, in All Things Considered. 2018, National Public Radio: Washington, DC.
  2. Felisa A. Smith, Rosemary E. Elliott Smith, S. Kathleen Lyons, and Jonathan L. Payne, Body size downgrading of mammals over the late Quaternary. Science, 360 (6386):310-313, 2018.



Dinosaur Tracks on Skye

Moat of what we know about dinosaurs comes from fossil remains, mainly skeletons.  But in the last century we have discovered other traces, including footprints [3].  Tracks are particularly interesting because they capture actual behavior in a particular time and place.

This spring Scottish researchers report on a new find of tracks from large sauropods that lived in middle Jurassic times [2].

The Sauropod footprints were left in a muddy, shallow lagoon (BBC, Jon Hoad)


Despite the epic Hollywood titles, there is relatively little known about the Jurassic period because there are relatively few areas with rocks from that era that might harbor fossils.  One place that does have Jurassic fossils is the Isle of Skye in Scotland.  In fact, the area has yielded many trackways, including the newly described find.

The remains are consistent with a shallow lagoon where wading animals left footprints on the soft bottom.  The tracks include 49 trackways that appear to be sauropods (lunch?), and some tridactyl tracks that are thought to be theropods (hunters?).

Unfortunately, it is difficult to know exactly what animals made the tracks, and the preservation is imperfect, as well.

With the overall collection of remains, it is clear that this area was inhabited by a variety of species, including dinosaurs.

At the very least, this study suggests that Skye will be an important source of information about the relatively unknown Jurassic era.

  1. BBC, Dinosaur tracks on Skye ‘globally important’, in BBC News -Scotland. 2018.
  2. Paige E. dePolo, Stephen L. Brusatte, Thomas J. Challands, Davide Foffa, Dugald A. Ross, Mark Wilkinson, and Hong-yu Yi, A sauropod-dominated tracksite from Rubha nam Brathairean (Brothers’ Point), Isle of Skye, Scotland. Scottish Journal of Geology, 2018.
  3. Martin Lockley, Tracking Dinosaurs: A New Look At An Ancient World, Cambridge, Cambridge University Press, 1991.