WFS News:Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs

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Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs

Citation: D’Emic MD, Whitlock JA, Smith KM, Fisher DC, Wilson JA (2013) Evolution of High Tooth Replacement Rates in Sauropod Dinosaurs. PLoS ONE 8(7): e69235. https://doi.org/10.1371/journal.pone.0069235

Editor: Alistair Robert Evans, Monash University, Australia

Abstract
Background

Tooth replacement rate can be calculated in extinct animals by counting incremental lines of deposition in tooth dentin. Calculating this rate in several taxa allows for the study of the evolution of tooth replacement rate. Sauropod dinosaurs, the largest terrestrial animals that ever evolved, exhibited a diversity of tooth sizes and shapes, but little is known about their tooth replacement rates.

Methodology/Principal Findings

Dental histology of the sauropod dinosaurs Camarasaurus and Diplodocus. Thin sections of Camarasaurus (A, C) and Diplodocus (B, D) premaxillary teeth showing incremental lines of von Ebner (white arrowheads) in dentin. Teeth are oriented with their long axis horizontal and the occlusal surface directed to the right. A shows the tip of tooth 3iii of Camarasaurus, and B shows the tip of tooth 4iv of Diplodocus. C and D are enlarged images of one ‘limb’ of tooth 3ii and 4iii, respectively. Abbreviations: edj, enamel-dentin junction; en, enamel; pc, pulp cavity. [planned for page width].

Dental histology of the sauropod dinosaurs Camarasaurus and Diplodocus.
Thin sections of Camarasaurus (A, C) and Diplodocus (B, D) premaxillary teeth showing incremental lines of von Ebner (white arrowheads) in dentin. Teeth are oriented with their long axis horizontal and the occlusal surface directed to the right. A shows the tip of tooth 3iii of Camarasaurus, and B shows the tip of tooth 4iv of Diplodocus. C and D are enlarged images of one ‘limb’ of tooth 3ii and 4iii, respectively. Abbreviations: edj, enamel-dentin junction; en, enamel; pc, pulp cavity. [planned for page width].

Cladogram of sauropodomorphs showing the optimization of key features related to elevated tooth replacement rates. The light gray field indicates taxa that have at least three replacement teeth at each tooth position; dark gray field encapsulates taxa that have narrow tooth crowns. Silhouettes along the top of the cladogram show the number and size of replacement teeth in one tooth position. These include (from left to right): Patagosaurus (MPEF-PV 1670), Mamenchisaurus [47], Diplodocus (this study), Nigersaurus [Sereno, Wilson, Witmer, Whitlock, Maga, Ide and Rowe, unpublished data], Camarasaurus (this study), and the Río Negro titanosaur (MPCA-79) [48]. Number of replacement teeth is unknown in Brachiosauridae, but the taxon is optimized to have had at least three. Cladogram based on [30] with the addition of Tazoudasaurus [49] and Bonitasaura [50]. [planned for column width].

Cladogram of sauropodomorphs showing the optimization of key features related to elevated tooth replacement rates.
The light gray field indicates taxa that have at least three replacement teeth at each tooth position; dark gray field encapsulates taxa that have narrow tooth crowns. Silhouettes along the top of the cladogram show the number and size of replacement teeth in one tooth position. These include (from left to right): Patagosaurus (MPEF-PV 1670), Mamenchisaurus [47], Diplodocus (this study), Nigersaurus [Sereno, Wilson, Witmer, Whitlock, Maga, Ide and Rowe, unpublished data], Camarasaurus (this study), and the Río Negro titanosaur (MPCA-79) [48]. Number of replacement teeth is unknown in Brachiosauridae, but the taxon is optimized to have had at least three. Cladogram based on [30] with the addition of Tazoudasaurus [49] and Bonitasaura [50]. [planned for column width].

We present tooth replacement rate, formation time, crown volume, total dentition volume, and enamel thickness for two coexisting but distantly related and morphologically disparate sauropod dinosaurs Camarasaurus and Diplodocus. Individual tooth formation time was determined by counting daily incremental lines in dentin. Tooth replacement rate is calculated as the difference between the number of days recorded in successive replacement teeth. Each tooth family in Camarasaurus has a maximum of three replacement teeth, whereas each Diplodocus tooth family has up to five. Tooth formation times are about 1.7 times longer in Camarasaurus than in Diplodocus (315 vs. 185 days). Average tooth replacement rate in Camarasaurus is about one tooth every 62 days versus about one tooth every 35 days in Diplodocus. Despite slower tooth replacement rates in Camarasaurus, the volumetric rate of Camarasaurus tooth replacement is 10 times faster than in Diplodocus because of its substantially greater tooth volumes. A novel method to estimate replacement rate was developed and applied to several other sauropodomorphs that we were not able to thin section.
Conclusions/Significance

Differences in tooth replacement rate among sauropodomorphs likely reflect disparate feeding strategies and/or food choices, which would have facilitated the coexistence of these gigantic herbivores in one ecosystem. Early neosauropods are characterized by high tooth replacement rates (despite their large tooth size), and derived titanosaurs and diplodocoids independently evolved the highest known tooth replacement rates among archosaurs.

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WFS News: Linking Geology and Microbiology

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Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

Citation: Haverkamp THA, Hammer Ø, Jakobsen KS (2014) Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure. PLoS ONE 9(1): e85990. https://doi.org/10.1371/journal.pone.0085990

Editor: Hauke Smidt, Wageningen University, Netherlands

Phylum level abundances of representative OTU sequences. The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.

Phylum level abundances of representative OTU sequences.
The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

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WFS News: Synthetic microorganisms and study of evolution

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Scientists at Scripps Research and their collaborators have created microorganisms that may recapitulate key features of organisms thought to have lived billions of years ago, allowing them to explore questions about how life evolved from inanimate molecules to single-celled organisms to the complex, multicellular lifeforms we see today.

By studying one of these engineered organisms-a bacterium whose genome consists of both ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)-the scientists hope to shed light on the early evolution of genetic material, including the theorized transition from a world where most life relied solely on the genetic molecule RNA to one where DNA serves as the primary storehouse of genetic information.

Using a second engineered organism, a genetically modified yeast containing an endosymbiotic bacterium, they hope to better understand the origins of cellular power plants called mitochondria. Mitochondria provide essential energy for the cells of eukaryotes, a broad group of organisms-including humans-that possesses complex, nucleus-containing cells.

 A genetically modified yeast containing an endosymbiotic bacterium. Credit: Scripps Research

A genetically modified yeast containing an endosymbiotic bacterium.Credit: Scripps Research

The researchers report engineering the microbes in two papers, one published October 29, 2018 in the Proceedings of the National Academy of Sciences (PNAS) and another published August 30, 2018 in Journal of the American Chemical Society (JACS).

“These engineered organisms will allow us to probe two key theories about major milestones in the evolution of living organisms-the transition from the RNA world to the DNA world and the transition from prokaryotes to eukaryotes with mitochondria,” says Peter Schultz, PhD, senior author on the papers and president of Scripps Research. “Access to readily manipulated laboratory models enables us to seek answers to questions about early evolution that were previously intractable.”

The origins of life on Earth have been a human fascination for millennia. Scientists have traced the arc of life back several billion years and concluded that the simplest forms of life emerged from Earth’s primordial chemical soup and subsequently evolved over the eons into organisms of greater and greater complexity. A monumental leap came with the emergence of DNA, a molecule that stores all of the information required to replicate life and directs cellular machinery to do its bidding primarily by generating RNA, which in turn directs the synthesis of proteins, the molecular workhorses in cells.

In the 1960s, Carl Woese and Leslie Orgel, along with DNA pioneer Francis Crick, proposed that before DNA, organisms relied on RNA to carry genetic information, a molecule similar to but far less stable than DNA, that can also catalyze chemical reactions like proteins. “In science class, students learn that DNA leads to RNA which in turn leads to proteins-that’s a central dogma of biology-but the RNA world hypothesis turns that on its head,” says Angad Mehta, PhD, first author of the new papers and a postdoctoral research associate at Scripps Research. “For the RNA world hypothesis to be true, you have to somehow get from RNA to a DNA genome, yet how that might have happened is still a very big question among scientists.”

One possibility is that the transition proceeded through a kind of microbial missing link, a replicating organism that stored genetic information as RNA. For the JACS study, the Scripps Research-led team created Escherichia coli bacteria that partially build their DNA with ribonucleotides, the molecular building blocks typically used to build RNA. These engineered genomes contained up to 50 percent RNA, thus simultaneously representing a new type of synthetic organism and possibly a throwback to billions of years ago.

Mehta cautions that their work so far has focused on characterizing this chimeric RNA-DNA genome and its effect on bacterial growth and replication but hasn’t explicitly explored questions about the transition from the RNA world to the DNA world. But, he says, the fact that E. coli with half its genome comprised of RNA can survive and replicate is remarkable and seems to support the possibility of the existence of evolutionarily transitional organisms possessing hybrid RNA-DNA genomes. The Scripps Research team is now studying how the mixed genomes of their engineered E. coli function and plans to use the bacteria to explore a number of evolutionary questions.

For instance, one question is whether the presence of RNA leads to rapid genetic drift-large changes in gene sequence in a population over time. Scientists theorize that massive genetic drift occurred quickly during early evolution, and the presence in the genome of RNA could help explain how genetic change occurred so quickly.

In the paper published in PNAS, the researchers report engineering another laboratory model for an evolutionary milestone thought to have occurred more than 1.5 billion years ago. They created a yeast dependent for energy on bacteria living inside it as a beneficial parasite or “endosymbiont.” This composite organism will allow them to investigate the ancient origins of mitochondria-tiny, bacteria-like organelles that produce chemical energy within the cells of all higher organisms.

Mitochondria are widely thought to have evolved from ordinary bacteria that were captured by larger, single-celled organisms. They carry out several key functions in cells. Most importantly, they serve as oxygen reactors, using O2 to make cells’ basic unit of chemical energy, the molecule ATP. As crucial as mitochondria are to cells, their origins remain somewhat mysterious, although there are clear hints of descent from a more independent organism, widely assumed to have been a bacterium.

Mitochondria have a double-membrane structure like that of some bacteria, and-again, like bacteria-contain their own DNA. Analyses of the mitochondrial genome suggest that it shares an ancient ancestor with modern Rickettsia bacteria, which can live within the cells of their hosts and cause disease. Stronger support for the bacterial origin of mitochondria theory would come from experiments showing that independent bacteria could indeed be transformed, in an evolution-like progression, into mitochondria-like symbionts. To that end, the Scripps Research scientists engineered E. coli bacteria that could live in, depend upon, and provide key assistance to, cells of Saccharomyces cerevisiae, also known as baker’s yeast.

The researchers started by modifying E. coli to lack the gene encoding thiamin, making the bacteria dependent on the yeast cells for this essential vitamin. At the same time, they added to the bacteria a gene for ADP/ATP translocase, a transporter protein, so that ATP produced within the bacterial cells would be supplied to their yeast-cell hosts-mimicking the central function of real mitochondria. The team also modified the yeast so that their own mitochondria were deficient at supplying ATP. Thus the yeast would be dependent on the bacteria for normal, mitochondria-based ATP production.

The team found that some of the engineered bacteria, after being modified with surface proteins to protect them from being destroyed in the yeast, lived and proliferated in harmony with their hosts for more than 40 generations and appeared to be viable indefinitely. “The modified bacteria seem to accumulate new mutations within the yeast to better adapt to their new surroundings,” says Schultz.

With this system established, the team will try to evolve the E. colito become mitochondria-like organelles. For the new E. coliendosymbiont, adapting to life inside yeast could allow it an opportunity to radically slim its genome. A typical E. coli bacterium, for example, has several thousand genes, whereas mitochondria have evolved a stripped-down set of just 37.

The Scripps Research team rounded out the study with further gene-subtraction experiments, and the results were promising: they found they could eliminate not just the E. coli thiamin gene but also the genes underlying the production of the metabolic molecule NAD and the amino acid serine, and still get a viable symbiosis.

“We are now well on our way to showing that we can delete the genes for making all 20 amino acids, which comprise a significant part of the E. coli genome,” says Schultz. “Once we’ve achieved that, we’ll move on to deleting genes for the syntheses of cofactors and nucleotides, and within a few years we hope to be able to get a truly minimal endosymbiotic genome.”

The researchers also hope to use similar endosymbiont-host systems to investigate other important episodes in evolution, such as the origin of chloroplasts, light-absorbing organelles that have a mitochondria-like role in supplying energy to plants.

Journal References:Angad P. Mehta, Yiyang Wang, Sean A. Reed, Lubica Supekova, Tsotne Javahishvili, John C. Chaput, Peter G. Schultz. Bacterial Genome Containing Chimeric DNA–RNA SequencesJournal of the American Chemical Society, 2018; 140 (36): 11464 DOI: 10.1021/jacs.8b07046

  1. Angad P. Mehta, Lubica Supekova, Jian-Hua Chen, Kersi Pestonjamasp, Paul Webster, Yeonjin Ko, Scott C. Henderson, Gerry McDermott, Frantisek Supek, Peter G. Schultz. Engineering yeast endosymbionts as a step toward the evolution of mitochondriaProceedings of the National Academy of Sciences, 2018; 201813143 DOI: 10.1073/pnas.1813143115

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New species of ‘missing link’ between dinosaurs and birds identified

Known as the ‘Icon of Evolution’ and ‘the missing link’ between dinosaurs and birds, Archaeopteryx has become one of the most famous fossil discoveries in Palaeontology.

Now, as part of an international team of scientists, researchers at The University of Manchester have identified a new species of Archaeopteryx that is closer to modern birds in evolutionary terms.

Dr John Nudds, from the University’s School of Earth and Environmental Sciences, and the team have been re-examining one of the only 12 known specimens by carrying out the first ever synchrotron examination, a form of 3D X-ray analysis, of an Archaeopteryx.

Dr. John Nudds with Archaeopteryx fossil specimen at the European Synchrotron in Grenoble. Credit: Image courtesy of The University of Manchester

Dr. John Nudds with Archaeopteryx fossil specimen at the European Synchrotron in Grenoble.
Credit: Image courtesy of The University of Manchester

Thanks to this new insight, the team says that this individual Archaeopteryx fossil, known as ‘specimen number eight’, is physically much closer to a modern bird than it is to a reptile. Therefore, it is evolutionary distinctive and different enough to be described as a new species — Archaeopteryx albersdoerferi.

The research, which is being published in journal Historical Biology, says that some of the differing skeletal characteristics of Archaeopteryx albersdoerferi include the fusion of cranial bones, different pectoral girdle (chest) and wing elements, and a reinforced configuration of carpals and metacarpals (hand) bones.

These characteristics are seen more in modern flying birds and are not found in the older Archaeopteryx lithographica species, which more resembles reptiles and dinosaurs.

Specimen number eight is the youngest of all the 12 known specimens by approximately half a million years. This age difference in comparison to the other specimens is a key factor in describing it as a new species.

Dr Nudds explains: “By digitally dissecting the fossil we found that this specimen differed from all of the others. It possessed skeletal adaptations which would have resulted in much more efficient flight. In a nutshell we have discovered what Archaeopteryx lithographica evolved into — i.e. a more advanced bird, better adapted to flying — and we have described this as a new species of Archaeopteryx.”

Archaeopteryx was first described as the ‘missing link’ between reptiles and birds in 1861 — and is now regarded as the link between dinosaurs and birds. Only 12 specimens have ever been found and all are from the late Jurassic of Bavaria, now Germany, dating back approximately 150 million years.

Lead author, Dr Martin Kundrát, from the University of Pavol Jozef Šafárik, Slovakia, said: “This is the first time that numerous bones and teeth of Archaeopteryx were viewed from all aspects including exposure of their inner structure. The use of synchrotron microtomography was the only way to study the specimen as it is heavily compressed with many fragmented bones partly or completely hidden in limestone.”

Dr Nudds added: “Whenever a missing link is discovered, this merely creates two further missing links — what came before, and what came after! What came before was discovered in 1996 with the feathered dinosaurs in China. Our new species is what came after. It confirms Archaeopteryx as the first bird, and not just one of a number of feathered theropod dinosaurs, which some authors have suggested recently. You could say that it puts Archaeopteryx back on its perch as the first bird!”

Citation: The University of Manchester. “New species of ‘missing link’ between dinosaurs and birds identified.” ScienceDaily. ScienceDaily, 25 October 2018. <www.sciencedaily.com/releases/2018/10/181025151820.htm>.

WFS News: Ancient flesh-eating fish look like piranha

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Scientists have unearthed the fossilised remains of a piranha-like species that they say is the earliest known example of a flesh-eating fish.This bony creature, found in South Germany, lived about 150 million years ago and had the distinctive sharp teeth of modern-day piranhas.These Jurassic marauders used their razor teeth to tear chunks of flesh and fins off other fish.Other fish were found nearby which had been attacked by the ancient piranhas.

This image shows a new piranha-like fish from Jurassic seas with sharp, pointed teeth that probably fed on the fins of other fish

This image shows a new piranha-like fish from Jurassic seas with sharp, pointed teeth that probably fed on the fins of other fish

“We have other fish from the same locality with chunks missing from their fins,” said Dr David Bellwood of James Cook University, Australia, who is one of the authors of the study.

“Feed on a fish and it is dead; nibble its fins and you have food for the future.”

The researchers analysed the jaws and found long pointed teeth on the exterior of a bone forming the roof of the mouth. They also found triangular teeth with serrated edges on bones that lie along the side of the lower-jaw.

The international team of scientists concluded that the pattern and shape of the teeth, jaw morphology and mechanics suggested a mouth well-equipped to slice flesh or fins.

An artist's impression of the ancient piranha

                                      An artist’s impression of the ancient piranha

“We were stunned that this fish had piranha-like teeth,” says Martina Kölbl-Ebert, of Jura-Museum Eichstätt, who led the study.

“It comes from a group of fishes (the pycnodontids) that are famous for their crushing teeth. It is like finding a sheep with a snarl like a wolf. But what was even more remarkable is that it was from the Jurassic.

“Fish as we know them, bony fishes, just did not bite flesh of other fishes at that time. Sharks have been able to bite out chunks of flesh but throughout history bony fishes have either fed on invertebrates or largely swallowed their prey whole. Biting chunks of flesh or fins was something that came much later.”

The study has been published in the journal, Current Biology.

Why is this important?

It shows the remarkable connection between the time when dinosaurs walked the Earth and our modern world. Piranhas attack other fish and tear chunks out of their fins and fin bases. The scientists found injuries in the same places on fish that had been attacked by the pre-historic piranhas some 150 million years ago.

“This is an amazing parallel with modern piranhas, which feed predominantly not on flesh but the fins of other fishes,” said Dr Bellwood.

“It’s a remarkably smart move as fins re-grow; a neat renewable resource.”

It also shows the value of studying fossils, as the area where the fish were found is among the best known fossil locations in the world but continues to throw up surprise findings like this one.

Source: BBC

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WFS News: Climate Change and the Geophysical Underpinnings of Species Diversity

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Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity

Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R2 = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5–95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust alternative to species-level predictions.

The geological classes and the lithologies included in each class.

        The geological classes and the lithologies included in each class.

Citation: Anderson MG, Ferree CE (2010) Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity. PLoS ONE 5(7): e11554. https://doi.org/10.1371/journal.pone.0011554

Editor: Justin Wright, Duke University, United States of America

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WFS News: Oldest skeleton of a fossil flying squirrel

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The oldest flying squirrel fossil ever found has unearthed new insight on the origin and evolution of these airborne animals.

Writing in the open-access journal eLife, researchers from the Institut Català de Paleontologia Miquel Crusafont (ICP) in Barcelona, Spain, described the 11.6-million-year-old fossil, which was discovered in Can Mata landfill, approximately 40 kilometers outside the city.

“Due to the large size of the tail and thigh bones, we initially thought the remains belonged to a primate,” says first author Isaac Casanovas-Vilar, researcher at the ICP. In fact, and much to the disappointment of paleoprimatologists, further excavation revealed that it was a large rodent skeleton with minuscule specialised wrist bones, identifying it as Miopetaurista neogrivensis — an extinct flying squirrel.

Combining molecular and paleontological data to carry out evolutionary analyses of the fossil, Casanovas-Vilar and the team demonstrated that flying squirrels evolved from tree squirrels as far back as 31 to 25 million years ago, and possibly even earlier.

In addition, their results showed that Miopetaurista is closely related to an existing group of giant flying squirrels called Petaurista. Their skeletons are in fact so similar that the large species that currently inhabits the tropical and subtropical forests of Asia could be considered living fossils.

The fossil flying squirrel Miopetaurista neogrivensis. (a) Reconstruction of the skeleton based in the partial skeleton IPS56468 from Abocador de Can Mata. Missing elements are based on extant giant flying squirrel Petaurista petaurista and are colored in blue. (b) Life appearance of Miopetaurista neogrivensis showing the animal ready to land on a tree branch. Coat pattern and color are based in extant Petaurista species, the sister taxon of Miopetaurista (see Figure 7). See Video 1 for an animated version of this reconstruction and 3D model in Supplementary file 1 to view and manipulate a low-quality model of the skeleton. For recovered elements of the postcranial skeleton see Figures 2 and 4 and Table 1. For a description and comparison of the postcranial bones, see Appendix 3.3. See Figure 6 and Video 3 for a more detailed cranial reconstruction. 3D models generated from µCT scan data and photogrammetry. Scale bar is 4 cm.

The fossil flying squirrel Miopetaurista neogrivensis.
(a) Reconstruction of the skeleton based in the partial skeleton IPS56468 from Abocador de Can Mata. Missing elements are based on extant giant flying squirrel Petaurista petaurista and are colored in blue. (b) Life appearance of Miopetaurista neogrivensis showing the animal ready to land on a tree branch. Coat pattern and color are based in extant Petaurista species, the sister taxon of Miopetaurista (see Figure 7). See Video 1 for an animated version of this reconstruction and 3D model in Supplementary file 1 to view and manipulate a low-quality model of the skeleton. For recovered elements of the postcranial skeleton see Figures 2 and 4 and Table 1. For a description and comparison of the postcranial bones, see Appendix 3.3. See Figure 6 and Video 3 for a more detailed cranial reconstruction. 3D models generated from µCT scan data and photogrammetry. Scale bar is 4 cm.

With 52 species scattered across the northern hemisphere, flying squirrels are the most successful group of mammals that adopted the ability to glide. To drift between trees in distances of up to 150 metres, these small animals pack their own ‘parachute’: a membrane draping between their lower limbs and the long cartilage rods that extend from their wrists. Their tiny, specialised wrist bones, which are unique to flying squirrels, help support the cartilaginous extensions.

But the origin of these animals is highly debated. While most genetic studies point towards the group splitting from tree squirrels about 23 million years ago, some 36-million-year-old remains that could belong to flying squirrels have previously been found. “The problem is that these ancient remains are mainly teeth,” Casanovas-Vilar explains. “As the dental features used to distinguish between gliding and non-gliding squirrels may actually be shared by the two groups, it is difficult to attribute the ancient teeth undoubtedly to a flying squirrel. In our study, we estimate that the split took place around 31 and 25 million years ago, earlier than previously thought, suggesting the oldest fossils may not belong to flying squirrels.

“Molecular and paleontological data are often at odds, but this fossil shows that they can be reconciled and combined to retrace history,” he adds. “Discovering even older fossils could help to retrace how flying squirrels diverged from the rest of their evolutionary tree.”

An exceptional site in a rubbish dump

The Can Mata landfill holds a set of more than 200 sites ranging in age between 12.6 and 11.4 Ma (middle to late Miocene). In the last 20 years, excavations carried out by the ICP in Can Mata have led to the identification of more than 80 species of mammals, birds, amphibians and reptiles. A remarkable number of primate remains from the site have revealed three new species of hominoids, nicknamed ‘Pau’ (Pierolapithecus catalaunicus), ‘Laia’ (Pliobates cataloniae) and ‘Lluc’ (Anoiapithecus brevirostris). Various studies of mammal remains recovered from the site, including the current work in eLife, indicate the existence of a dense subtropical forest.

  1. Isaac Casanovas-Vilar, Joan Garcia-Porta, Josep Fortuny, Óscar Sanisidro, Jérôme Prieto, Marina Querejeta, Sergio Llácer, Josep M Robles, Federico Bernardini, David M Alba. Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the groupeLife, 2018; 7 DOI: 10.7554/eLife.39270

Source: ScienceDaily.com

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WFS News: Dinosaur from the Earliest Jurassic of South Africa

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A Giant Dinosaur from the Earliest Jurassic of South Africa and the Transition to Quadrupedality in Early Sauropodomorphs

A new species of a giant dinosaur has been found in South Africa’s Free State Province. The plant-eating dinosaur, named Ledumahadi mafube, weighed 12 tonnes and stood about four metres high at the hips. Ledumahadi mafube was the largest land animal alive on Earth when it lived, nearly 200 million years ago. It was roughly double the size of a large African elephant.

A team of international scientists, led by University of the Witwatersrand (Wits) palaeontologist Professor Jonah Choiniere, described the new species in the journal Current Biology today.

The dinosaur’s name is Sesotho for “a giant thunderclap at dawn” (Sesotho is one of South Africa’s 11 official languages and an indigenous language in the area where the dinosaur was found).

Ledumahadi mafube is the first of the giant sauropodomorphs of the Jurassic. Credit: Wits University

Ledumahadi mafube is the first of the giant sauropodomorphs of the Jurassic.Credit: Wits University

“The name reflects the great size of the animal as well as the fact that its lineage appeared at the origins of sauropod dinosaurs,” said Choiniere. “It honours both the recent and ancient heritage of southern Africa.”

Ledumahadi mafube is one of the closest relatives of sauropod dinosaurs. Sauropods, weighing up to 60 tonnes, include well-known species like Brontosaurus. All sauropods ate plants and stood on four legs, with a posture like modern elephants. Ledumahadi evolved its giant size independently from sauropods, and although it stood on four legs, its forelimbs would have been more crouched. This caused the scientific team to consider Ledumahadi an evolutionary “experiment” with giant body size.

Ledumahadi‘s fossil tells a fascinating story not only of its individual life history, but also the geographic history of where it lived, and of the evolutionary history of sauropod dinosaurs.

“The first thing that struck me about this animal is the incredible robustness of the limb bones,” says lead author, Dr Blair McPhee. “It was of similar size to the gigantic sauropod dinosaurs, but whereas the arms and legs of those animals are typically quite slender, Ledumahadi‘s are incredibly thick. To me this indicated that the path towards gigantism in sauropodomorphs was far from straightforward, and that the way that these animals solved the usual problems of life, such as eating and moving, was much more dynamic within the group than previously thought.”

The research team developed a new method, using measurements from the “arms” and “legs” to show that Ledumahadi walked on all fours, like the later sauropod dinosaurs, but unlike many other members of its own group alive at its time such as Massospondylus. The team also showed that many earlier relatives of sauropods stood on all fours, that this body posture evolved more than once, and that it appeared earlier than scientists previously thought.

“Many giant dinosaurs walked on four legs but had ancestors that walked on two legs. Scientists want to know about this evolutionary change, but amazingly, no-one came up with a simple method to tell how each dinosaur walked, until now,” says Dr Roger Benson.

By analysing the fossil’s bone tissue through osteohistological analysis, Dr Jennifer Botha-Brink from the South African National Museum in Bloemfontein established the animal’s age.

“We can tell by looking at the fossilised bone microstructure that the animal grew rapidly to adulthood. Closely-spaced, annually deposited growth rings at the periphery show that the growth rate had decreased substantially by the time it died,” says Botha-Brink. This indicates that the animal had reached adulthood.

“It was also interesting to see that the bone tissues display aspects of both basal sauropodomorphs and the more derived sauropods, showing that Ledumahadi represents a transitional stage between these two major groups of dinosaurs.”

Ledumahadi lived in the area around Clarens in South Africa’s Free State Province. This is currently a scenic mountainous area, but looked much different at that time, with a flat, semi-arid landscape and shallow, intermittently dry streambeds.

“We can tell from the properties of the sedimentary rock layers in which the bone fossils are preserved that 200 million years ago most of South Africa looked a lot more like the current region around Musina in the Limpopo Province of South Africa, or South Africa’s central Karoo,” says Dr Emese Bordy.

Ledumahadi is closely related to other gigantic dinosaurs from Argentina that lived at a similar time, which reinforces that the supercontinent of Pangaea was still assembled in the Early Jurassic. “It shows how easily dinosaurs could have walked from Johannesburg to Buenos Aires at that time,” says Choiniere.

South Africa’s Minister of Science and Technology Mmamoloko Kubayi-Ngubane says the discovery of this dinosaur underscores just how important South African palaeontology is to the world.

“Not only does our country hold the Cradle of Humankind, but we also have fossils that help us understand the rise of the gigantic dinosaurs. This is another example of South Africa taking the high road and making scientific breakthroughs of international significance on the basis of its geographic advantage, as it does in astronomy, marine and polar research, indigenous knowledge, and biodiversity,” says Kubayi-Ngubane.

The research team behind Ledumahadi includes South African-based palaeoscientists, Dr Emese Bordy and Dr Jennifer Botha-Brink, from the University of Cape Town and the South African National Museum in Bloemfontein, respectively.

The project also had a strong international component with the collaboration of Professor Roger BJ Benson of Oxford University and Dr Blair McPhee, currently residing in Brazil.

“South Africa employs some of the world’s top palaeontologists and it was a privilege to be able to build a working group with them and leading researchers in the UK,” says Choiniere, who recently emigrated from the USA to South Africa. “Dinosaurs didn’t observe international boundaries and it’s important that our research groups don’t either.”

Video: https://www.youtube.com/watch?v=Q8FHxPocwDM

Journal Reference: Blair W. McPhee, Roger B.J. Benson, Jennifer Botha-Brink, Emese M. Bordy, Jonah N. Choiniere. A Giant Dinosaur from the Earliest Jurassic of South Africa and the Transition to Quadrupedality in Early Sauropodomorphs. Current Biology, 2018; DOI: 10.1016/j.cub.2018.07.063

@ WFS,World Fossil Society,Riffin T Sajeev,Russel T Sajeev

WFS News:Description of climate-envelope models

@WFS,World Fossil Society,Riffin T Sajeev,Russel T Sajeev

Climate-envelope models attempt to capture the climatic conditions that constrain the potential niche of
a species, and use them to predict the probability of occurrence of species in an area. There are many
different types of climate-envelope models [1], distinguished among other things by the type of data
they use and the type of predictions that can make [2]. The performance of climate-envelope models
can also vary depending on the characteristics of the data [3–5]. Thus, we applied three different types
of models, each with its own strengths and weaknesses, and then averaged their predictions weighted
by their respective predictive performances (evaluated with the true skill statistic).

BIOCLIM was one of the first algorithms used to model species distributions [6], and is one of a small
family of climate-envelope models that rely only on presence data (fossils are necessarily presenceonly
data). Other methods require the use of ‘background’ or absence data (known or suspected points
in space where the species is/was absent), but BIOCLIM simply describes the climate envelope of a
species as the multidimensional niche between the extreme conditions in which the species has been
observed. It can rank the suitability of an area as a function of how far the climatic conditions of a site
are from the median climatic conditions in which the species has been observed. Because it is simple
and requires few assumptions compared to other methods, it has been recommended for modelling
palaeo-distributions based on fossil records [7].
MaxEnt [8] has become one of the most popular methods to model species distributions with presenceonly
data due to its general good performance [9]. The method is based in the principle of maximum
entropy, which states that from an infinity of possible climate envelopes with a common set of
constraints, the one with the maximum entropy should be preferred (see refs 9 and 10 for a detailed
statistical description of MaxEnt). For example, constraints could be that the climate envelope of a
species should have the same mean or median as the climates in which the species was observed.
However, there is an infinite number of different climate envelopes that produce the same median or
mean. Thus, of all the possibilities, the one with the maximum entropy (i.e., closest to a uniform
distribution) should prevail. To determine which climate envelope has maximum entropy, the climates
in which the species has been observed as well as the availability of climates throughout the study
region must be known. As such, MaxEnt is called a presence-background method, in contrast to
BIOCLIM.

The binomial generalised linear model represents a powerful technique to model not only the
occurrence of species, but almost any phenomenon with a binary response [11]. In contrast to
BIOCLIM and MaxEnt however, generalised linear models require presence and absence data. While
the background data used by MaxEnt are not assumed to be places where the species is truly absent, the
absences used in generalised linear models are. This can be troublesome even when absences have been
recorded during field surveys [12], and even more so when true absence data are lacking. Nonetheless,
it is common to select pseudo-absences from the background area for generalised linear models
[13,14]. Pseudo-absences are points where the species has not been observed and are assumed to be
absences. Selecting pseudo-absences in a way that minimizes the risk of having false absences (e.g., by
selecting them from places with climates in which the species has not been observed) or that accounts
for spatial biases in the sampling effort can improve the performance of climate-envelope models [14],
but sometimes simply picking pseudo-absences randomly results in the best predictions [15].

References
1. Elith J, Graham CH, Anderson RP, Dudik M, Ferrier S, Guisan A, et al. Novel methods improve
prediction of species’ distributions from occurrence data. Ecography. 2006;29: 129–151.
doi:10.1111/j.2006.0906-7590.04596.x
2. Guillera-Arroita G, Lahoz-Monfort J, Elith J, Gordon A, Kujala H, Lentini P, et al. Is my species
distribution model fit for purpose? Matching data and models to applications. Glob Ecol
Biogeogr. 2015; 276–292. doi:10.1111/geb.12268
3. Miller J. Virtual species distribution models: Using simulated data to evaluate aspects of model
performance. Prog Phys Geogr. 2014;38: 117–128. doi:10.1177/0309133314521448
4. Stockwell DRB, Peterson AT. Effects of sample size on accuracy of species distribution models.
Ecol Modell. 2002;148: 1–13. doi:10.1016/S0304-3800(01)00388-X
5. Elith J, Leathwick JR. Species Distribution Models: Ecological Explanation and Prediction
Across Space and Time. Annu Rev Ecol Evol Syst. 2009;40: 677–697.
doi:10.1146/annurev.ecolsys.110308.120159
6. Booth TH, Nix HA, Busby JR, Hutchinson MF. Bioclim: The first species distribution modelling
package, its early applications and relevance to most current MaxEnt studies. Divers Distrib.
2014;20: 1–9. doi:10.1111/ddi.12144
7. Varela S, Lobo JM, Hortal J. Using species distribution models in paleobiogeography: A matter
of data, predictors and concepts. Palaeogeogr Palaeoclimatol Palaeoecol. 2011;310: 451–463. doi:10.1016/j.palaeo.2011.07.021
8. Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic
distributions. Ecol Modell. 2006;190: 231–259. doi:10.1016/j.ecolmodel.2005.03.026
9. Merow C, Smith MJ, Silander JA. A practical guide to MaxEnt for modeling species’
distributions: What it does, and why inputs and settings matter. Ecography. 2013;36: 1058–1069.
doi:10.1111/j.1600-0587.2013.07872.x
10. Elith J, Phillips SJ, Hastie T, Dudík M, Chee YE, Yates CJ. A statistical explanation of MaxEnt
for ecologists. Divers Distrib. 2011;17: 43–57. doi:10.1111/j.1472-4642.2010.00725.x
11. Austin MP. Spatial prediction of species distribution: an interface between ecological theory and
statistical modelling. Ecol Modell. 2002;157: 101–118. doi:10.1016/S0304-3800(02)00205-3
12. Lobo JM, Jiménez-Valverde A, Hortal J. The uncertain nature of absences and their importance
in species distribution modelling. Ecography. 2010;33: 103–114. doi:10.1111/j.1600-
0587.2009.06039.x
13. Elith J, Leathwick J. Predicting species distributions from museum and herbarium records using
multiresponse models fitted with multivariate adaptive regression splines. Divers Distrib.
2007;13: 265–275. doi:10.1111/j.1472-4642.2007.00340.x
14. Iturbide M, Bedia J, Herrera S, del Hierro O, Pinto M, Gutiérrez JM. A framework for species
distribution modelling with improved pseudo-absence generation. Ecol Modell. 2015;312: 166–
174. doi:10.1016/j.ecolmodel.2015.05.018
15. Sequeira A, Mellin C, Rowat D, Meekan MG, Bradshaw CJA. Ocean-scale prediction of whale
shark distribution. Divers Distrib. 2012;18: 504–518. doi:10.1111/j.1472-4642.2011.00853.x

Source: Block S, Saltré F, Rodríguez-Rey M, Fordham DA, Unkel I, Bradshaw CJA (2016) Where to Dig for Fossils: Combining Climate-Envelope, Taphonomy and Discovery Models. PLoS ONE 11(3): e0151090. https://doi.org/10.1371/journal.pone.0151090

Editor: Peter Wilf, Penn State University, UNITED STATES

@WFS,World Fossil Society,Riffin T Sajeev,Russel T Sajeev

Plate tectonics may have been active on Earth since its origin

A new study suggests that plate tectonics — a scientific theory that divides Earth into large chunks of crust that move slowly over hot viscous mantle rock — could have been active from the planet’s very beginning. The new findings defy previous beliefs that tectonic plates were developed over the course of billions of years.

The paper, published in Earth and Planetary Science Letters, has important implications in the fields of geochemistry and geophysics. For example, a better understanding of plate tectonics could help predict whether planets beyond our solar system could be hospitable to life.

“Plate tectonics set up the conditions for life,” said Nick Dygert, assistant professor of petrology and geochemistry in UT’s Department of Earth and Planetary Sciences and coauthor of the study. “The more we know about ancient plate tectonics, the better we can understand how Earth got to be the way it is now.”

For the research, Dygert and his team looked into the distribution of two very specific noble gas isotopes: Helium-3 and Neon-22. Noble gases are those that don’t react to any other chemical element.

Previous models have explained Earth’s current Helium-3/Neon-22 ratio by arguing that a series of large-scale impacts (like the one that produced our moon) resulted in massive magma oceans, which degassed and incrementally increased the ratio each time.

However, Dygert believes the scenario is unlikely.

“While there is no conclusive evidence that this didn’t happen,” he said, “it could have only raised the Earth’s Helium-3/Neon-22 ratio under very specific conditions.”

Instead, Dygert and his team believe the Helium-3/Neon-22 ratio raised in a different way.

As Earth’s crust is continuously formed, the ratio of helium to neon in the mantle beneath the crust increases. By calculating this ratio in the mantle beneath the crust, and considering how this process would affect the bulk Earth over long periods of time, a rough timeline of Earth’s tectonic plate cycling can be established.

“Helium-3 and Neon-22 were produced during the formation of the solar system and not by other means,” Dygert said. “As such, they provide valuable insight into Earth’s earliest conditions and subsequent geologic activity.”

Citation: University of Tennessee at Knoxville. “Plate tectonics may have been active on Earth since the very beginning.” ScienceDaily. ScienceDaily, 26 September 2018. <www.sciencedaily.com/releases/2018/09/180926192044.htm>.