Bat faeces and biodiversity in Indonesia

This 2015 video says about itself:

Bat Man of Borneo | Expedition Raw

Braving guano, urine, and infectious diseases is all in a day’s work for bat ecologist Donald McFarlane, who descends into the depths of Borneo’s Gomantong Caves [in Malaysia] to study the bats that live there.

From James Cook University in Australia:

Holy Pleistocene Batman, the answer’s in the cave

Let’s say you wanted to solve a 20,000-year-old mystery, where would you start?

April 25, 2019

Summary: Examining a 3-meter stack of bat feces has shed light on the landscape of the ancient continent of Sundaland. The research could help explain the biodiversity of present-day Borneo, Sumatra, and Java. It could also add to our understanding of how people moved through the region.

Let’s say you wanted to solve a 20,000-year-old mystery, where would you start? Perhaps archaeology and geology come to mind. Or, you could sift through a 3-metre pile of bat faeces.

Researchers from James Cook University in Cairns, Australia, chose the bat poo in their quest to answer to a long-standing question: why is there some much biodiversity on the islands of Sumatra, Borneo and Java, when not so long ago (geologically speaking) they were all part of one vast continent?

One theory has been that the former continent (Sundaland) was dissected by a savanna corridor. “That might explain why Sumatra and Borneo each have their own species of orang-utan, even though they were linked by land for millions of years,” Dr Chris Wurster said. “The corridor would have divided the two separate rainforest refuges, as the sea does now.”

The corridor theory has been boosted by millions of insect-eating bats, which have gathered evidence about the landscape over millennia and deposited it in layers in their caves.

“Bat poo is highly informative, and especially so in the tropics, where the climate can make some of the more traditional modes of investigation less available,” Dr Wurster said.

A three-metre pile of bat faeces at Salah Cave in Borneo gave the researchers a 40,000-year-old record composed of insect skeletons.

“We can’t tell what insects the bats were eating throughout that time, because they’re in tiny fragments, but we can read the chemistry,” Dr Wurster said.

“Eating insects that have been feeding on tropical grasses results in faeces with a characteristic chemical imprint. It’s quite different from the result you’d get from eating insects that fed on tropical trees.”

According to the bat record the landscape around Saleh Cave (now featuring lush rainforest) was once dominated by tropical grasses.

“Combined with other cave studies in the region, this leads us to support the corridor theory, and also gives us some confidence as to the extent of the corridor,” Dr Wurster said.

The corridor could also shed light on human pre-history.

“A savanna corridor, which would be much more easily traversed than rainforest, might help to explain how people moved relatively quickly through this region and on to Australia and New Guinea.”

‘Savanna in equatorial Borneo during the late Pleistocene’ is published in the latest edition of Scientific Reports.

Dr Chris Wurster is a Senior Research Associate at James Cook University, specialising in stable isotope geochemistry.


Aquatic ankylosaur dinosaur discovery?

This 21 April 2019 video says about itself:

An Aquatic Ankylosaur?

There were once some very strange dinosaurs, but one of the strangest may have been a species of small, possibly fish-eating aquatic ankylosaurLiaoningosaurus paradoxus.

Big prehistoric carnivore discovered in Kenyan museum

This 18 April 2019 video is called Newly Discovered Ancient Carnivore Was Bigger Than a Polar Bear.

From Ohio University in the USA:

Fossils found in museum drawer in Kenya belong to gigantic carnivore

Paleontologists say mammal was larger than a polar bear

April 18, 2019

Paleontologists at Ohio University have discovered a new species of meat-eating mammal larger than any big cat stalking the world today. Larger than a polar bear, with a skull as large as that of a rhinoceros and enormous piercing canine teeth, this massive carnivore would have been an intimidating part of the eastern African ecosystems occupied by early apes and monkeys.

In a new study published in the Journal of Vertebrate Paleontology, the researchers name Simbakubwa kutokaafrika, a gigantic carnivore known from most of its jaw, portions of its skull, and parts of its skeleton. The 22-million-year-old fossils were unearthed in Kenya decades ago as researchers canvassed the region searching for evidence of ancient apes. Specimens were placed in a drawer at the National Museums of Kenya and not given a great deal of attention until Ohio University researchers Dr. Nancy Stevens and Dr. Matthew Borths rediscovered them, recognizing their significance.

“Opening a museum drawer, we saw a row of gigantic meat-eating teeth, clearly belonging to a species new to science,” says study lead author Borths. Borths was a National Science Foundation Postdoctoral Research Fellow with Stevens in the Department of Biomedical Sciences at Ohio University when the research was conducted, and is now Curator of the Division of Fossil Primates at the Duke Lemur Center at Duke University.

Simbakubwa is Swahili for “big lion” because the animal was likely at the top of the food chain in Africa, as lions are in modern African ecosystems. Yet Simbakubwa was not closely related to big cats or any other mammalian carnivore alive today. Instead, the creature belonged to an extinct group of mammals called hyaenodonts.

Hyaenodonts were the first mammalian carnivores in Africa. For about 45 million years after the extinction of the non-avian dinosaurs, hyaenodonts were the apex predators in Africa. Then, after millions of years of near-isolation, tectonic movements of the Earth’s plates connected Africa with the northern continents, allowing floral and faunal exchange between landmasses. Around the time of Simbakubwa, the relatives of cats, hyenas, and dogs began to arrive in Africa from Eurasia.

As the relatives of cats and dogs were going south, the relatives of Simbakubwa were going north. “It’s a fascinating time in biological history,” Borths says. “Lineages that had never encountered each other begin to appear together in the fossil record.”

The species name, kutokaafrika, is Swahili for “coming from Africa” because Simbakubwa is the oldest of the gigantic hyaenodonts, suggesting this lineage of giant carnivores likely originated on the African continent and moved northward to flourish for millions of years.

Ultimately, hyaenodonts worldwide went extinct. Global ecosystems were changing between 18 and 15 million years ago as grasslands replaced forests and new mammalian lineages diversified. “We don’t know exactly what drove hyaenodonts to extinction, but ecosystems were changing quickly as the global climate became drier. The gigantic relatives of Simbakubwa were among the last hyaenodonts on the planet,” remarks Borths.

“This is a pivotal fossil, demonstrating the significance of museum collections for understanding evolutionary history,” notes Stevens, Professor in the Heritage College of Osteopathic Medicine at Ohio University and co-author of the study. “Simbakubwa is a window into a bygone era. As ecosystems shifted, a key predator disappeared, heralding Cenozoic faunal transitions that eventually led to the evolution of the modern African fauna.”

This study was funded by grants from the National Science Foundation (EAR/IF-0933619; BCS-1127164; BCS-1313679; EAR-1349825; BCS-1638796; DBI-1612062), The Leakey Foundation, National Geographic Society (CRE), Ohio University Research Council, Ohio University Heritage College of Osteopathic Medicine, SICB and The Explorers Club.

This discovery underscores both the importance of supporting innovative uses of fossil collections, as well as the importance of supporting the research and professional development of talented young postdoctoral scientists like Dr. Borths,” said Daniel Marenda, a program director at the National Science Foundation, which funded this research. “This work has the potential to help us understand how species adapt — or fail to adapt in this case — to a rapidly changing global climate.”

Beetle-ant symbiosis in the dinosaur age

Detailed photos of the newly discovered Promyrmister kistneri beetle's morphology through its amber encasement. Credit: Courtesy of the Parker laboratory / eLife

From the California Institute of Technology in the USA:

These beetles have successfully freeloaded for 100 million years

Ancient beetle infiltrated earliest-known ant colonies like its modern relatives

April 17, 2019

Summary: An ancient and rare beetle fossil is the oldest example of a social relationship between two animal species.

Almost 100 million years ago, a tiny and misfortunate beetle died after wandering into a sticky glob of resin leaking from a tree in a region near present-day Southeast Asia. Fossilized in amber, this beetle eventually made its way to the desk of entomologist Joe Parker, assistant professor of biology and biological engineering at Caltech. Parker and his colleagues have now determined that the perfectly preserved beetle fossil is the oldest-known example of an animal in a behaviorally symbiotic relationship.

A paper describing the work appears on April 16 in the journal eLife.

Symbiotic relationships between two species have arisen repeatedly during animal evolution. These relationships range from mutually beneficial associations, like humans and their pet dogs, to the parasitic, like a tapeworm and its host.

Some of the most complex examples of behavioral symbiosis occur between ants and other types of small insects called myrmecophiles — meaning “ant lovers.” Thanks to ants’ abilities to form complex social colonies, they are able to repel predators and amass food resources, making ant nests a highly desirable habitat. Myrmecophiles display elaborate social behaviors and chemical adaptations to deceive ants and live among them, reaping the benefits of a safe environment and plentiful food.

Ants’ social behaviors first appear in the fossil record 99 million years ago, during the Cretaceous period of the Mesozoic era, and are believed to have evolved not long before, in the Early Cretaceous. Now, the discovery of a Cretaceous myrmecophile fossil implies that the freeloading insects were already taking advantage of ants’ earliest societies. The finding means that myrmecophiles have been a constant presence among ant colonies from their earliest origins and that this socially parasitic lifestyle can persist over vast expanses of evolutionary time.

“This beetle-ant relationship is the most ancient behavioral symbiosis now known in the animal kingdom,” says Parker. “This fossil shows us that symbiosis can be a very successful long-term survival strategy for animal lineages.”

The fossilized beetle, named Promyrmister kistneri, belongs to a subfamily of “clown” beetles (Haeteriinae), all modern species of which are myrmecophiles. These modern beetles are so specialized for life among ants that they will die without their ant hosts and have evolved extreme adaptations for infiltrating colonies. The beetles are physically well protected by a thick tank-like body plan and robust appendages, and they can mimic their host ants’ nest pheromones, allowing them to disguise themselves in the colony. They also secrete compounds that are thought to be pacifying or attractive to ants, helping the beetles gain the acceptance of their aggressive hosts. The fossilized Promyrmister is a similarly sturdy insect, with thick legs, a shielded head, and glandular orifices that the researchers theorize exuded chemicals to appease its primitive ant hosts.

Depending on another species so heavily for survival has its risks; indeed, an extinction of the host species would be catastrophic for the symbiont. The similarities between the fossilized beetle and its modern relatives suggest that the particular adaptations of myrmecophile clown beetles first evolved inside colonies of early “stem group” ants, which are long extinct. Due to Promyrmister’s remarkable similarity to modern clown beetles, Parker and his collaborators infer that the beetles must have “host switched” to colonies of modern ants to avoid undergoing extinction themselves. This adaptability of symbiotic organisms to move between partner species during evolution may be essential for the long-term stability of these intricate interspecies relationships.

What coelacanths tell about brain evolution

This 2 February 2018 video says about itself:

Diving With Coelacanths

This video is part of the banquet presentation given by Richard Pyle at the 2013 Marine Aquarium Conference of North America (MACNA) in Ft. Lauderdale, Florida. It represents a video overview of a series of dives conducted in 2011 off Sodwana Bay, South Africa, to find and film living Coelacanths.

The video also shows what the habitat looks like at depths of 100-120 meters (330-400 feet) off Sodwana Bay. The dives were led by Peter Timm, and filmed by Robert Whitton, Daniel Stevenson and Richard Pyle.

From the European Synchrotron Radiation Facility:

Coelacanth reveals new insights into skull evolution

April 17, 2019

An international team of researchers presents the first observations of the development of the skull and brain in the living coelacanth Latimeria chalumnae. Their study, published in Nature, provides new insights into the biology of this iconic animal and the evolution of the vertebrate skull.

The coelacanth Latimeria is a marine fish closely related to tetrapods, four-limbed vertebrates including amphibians, mammals and reptiles. Coelacanths were thought to have been extinct for 70 million years, until the accidental capture of a living specimen by a South African fisherman in 1938. Eighty years after its discovery, Latimeria remains of scientific interest for understanding the origin of tetrapods and the evolution of their closest fossil relatives — the lobe-finned fishes.

One of the most unusual features of Latimeria is its hinged braincase, which is otherwise only found in many fossil lobe-finned fishes from the Devonian period (410-360 million years ago). The braincase of Latimeria is completely split into an anterior and posterior portion by a joint called the “intracranial joint.” In addition, the brain lies far at the rear of the braincase and takes up only 1% of the cavity housing it. This mismatch between the brain and its cavity is totally unequalled among living vertebrates. How the coelacanth skull grows and why the brain remains so small has puzzled scientists for years. To answer these questions, researchers studied specimens at different stages of cranial development from several public natural history collections.

Although many specimens of adult coelacanths are available in natural history collections, earlier life stages such as fetuses are extremely rare. Scientists hence used state-of-the-art imaging techniques to visualize the internal anatomy of the specimens without damaging them. They notably digitalized a 5 cm-long fetus, the earliest developmental stage available for Latimeria, with synchrotron X-ray microtomography at the European Synchrotron (ESRF). Over the last two decades, the ESRF has developed unique expertise in designing non-invasive techniques widely used for evolutionary biology studies.

In addition, the researchers also imaged other stages with a powerful Magnetic Resonance Imaging (MRI) scanner at the Brain and Spine Institute (Paris, France), and a conventional X-ray micro-CTscan at the Muséum national d’Histoire naturelle (Paris, France). These data were used to generate detailed 3D models, which allowed scientists to describe how the form of the skull, the brain and the notochord (a tube extending below the brain and the spinal cord in the early stages of life) changes from a fetus to an adult.

They also observed how these structures are positioned relative to each other at each stage, and compared their observations with what is known about the formation of the skull in other vertebrates.

In contrast to most other vertebrates, where the notochord is replaced by the vertebral column early in embryonic development, the notochord expands considerably in Latimeria. The dramatic enlargement of the notochord likely influences the patterning of the braincase, and might underpin the formation of the intracranial joint. The brain might also be affected by the enlargement of the notochord, as relative size dramatically decreases during development.

These results illuminate for the first time the development of the living coelacanth skull and brain, and open up new avenues for research on the evolution of the vertebrate head.

Hugo Dutel, lead author and research associate in palaeobiology at the University of Bristol, UK, says, “These are very unique observations, but they represent only a tiny step forward compared to the amount we know on the development of other species. There are still more questions than answers! Latimeria still holds many clues for our understanding of vertebrate evolution, and it is important to protect this threatened species and its environment.”

Flightless birds evolution, new research

This 2016 video is called TOP 10 FLIGHTLESS BIRDS.

From Harvard University in the USA:

Genetics behind the evolution of flightless birds

April 17, 2019

Summary: Based on the analysis of the genomes of more than a dozen flightless birds, including an extinct moa, researchers found that while different species show wide variety in the protein-coding portions of their genome, they appear to turn to the same regulatory pathways when evolving flight loss.

Since Darwin’s era, scientists have wondered how flightless birds like emus, ostriches, kiwi, cassowaries and others are related, and for decades the assumption was that they must all share a common ancestor who abandoned the skies for a more grounded life.

By the early 2000s, new research using genetic tools upended that story, and instead pointed to the idea that flighlessness evolved many times throughout history. Left unanswered, however, were questions about whether evolution had pulled similar or different genetic levers in each of those independent avian lineages.

A team of Harvard researchers believes they may now have part of the answer.

Based on the analysis of the genomes of more than a dozen flightless birds, including an extinct moa, a team of researchers led by Tim Sackton, Director of Bioinformatics for the FAS Informatics Group and Professor of Organismic and Evolutionary Biology Scott Edwards found that while different species show wide variety in the protein-coding portions of their genome, they appear to turn to the same regulatory pathways when evolving flight loss. The study is described in an April 5 paper published in Science.

In addition to Sackton and Edward, the study was co-authored by Professor of Statistics and Professor of Biostatistics Jun Liu, Statistics research assistant Zhirui Hu, Alison Cloutier, a post-doctoral researcher working in Edwards’ lab, and teams from New Zealand, University of Texas at Austin, and the Royal Ontario Museum.

“There is a long history in evolutionary biology of converging traits — the idea that there’s independent evolution toward the same kind of phenotype,” Sackton said. “What we were interested in is how does that happen?

“These birds all have a similar body plan,” he continued. “They have reduced forelimbs, to different degrees, and they all have this loss of the ‘keel’ in their breastbone that anchors flight muscles. What that amounts to is a suite of convergent morphological changes that led to this similar body plan across all these species.”

To understand what drove that suite of changes, Sackton, Edwards and colleagues turned to the genomes of the birds themselves.

“We wanted to compare not just the parts of the genome that code for proteins, but also the parts of the genome that regulate when those proteins are expressed,” Sackton said, of the various species examined for the study. To identify those regions, the team used a process that involved aligning the genomes of more than three dozen bird species — both flying and flightless — and then identifying regions that showed relatively few differences in their genetic sequence. These places in the genome that are conserved, but not part of proteins, are likely to have a regulatory function.

“We worked with collaborators in Statistics here at Harvard to develop a new statistical method that allowed us to ask, for each of those regulatory elements, how many of these species showed the same pattern of divergence, suggesting they have changed the same regulatory elements,” Sackton said. “And what we found was that, while there is not much sharing of protein-coding genes, there is for these regulatory regions, suggesting that there are shared developmental pathways that are repeatedly targeted every time this phenotype has evolved.”

While the protein-coding genes appear to be responsible for adaptations in diet, feather function and environment, Sackton said, the regulatory regions seem to play a key role in the body-scaling changes that go along with flight loss.

“What’s interesting about the morphological changes…is they have to preserve their hindlimbs,” he said. “There are lots of ways to stop a limb from forming, but shrinking a forelimb without changing the hindlimb is more difficult.”

And in some ways, Sackton said, that story makes sense — strange as it may seem, it is likely easier to not form a limb versus shrinking one.

“If you think about it, there’s lots of ways to break something,” he said. “There are a bunch of steps early in limb development where, if a protein doesn’t get expressed, it’ll just turn the system off and you don’t get a limb.

“But this is actually a complicated shift in body scaling,” he continued. “You can’t just willy-nilly grow limbs to different sizes, so…the fact that it’s important they maintain functional hindlimbs constrains the system and might be why we see this convergent pattern.”

To prove that theory, the team tagged certain regulatory regions in the birds’ genomes with a gene that would produce green fluorescent protein, and found that — in flightless species, where those regions where believed to have undergone functional changes — the marker gene was effectively turned off.

“To get a limb to start growing, a bunch of things need to happen…so if you can knock out an enhancer and make it harder for those proteins to be expressed you can delay that process,” Sackton said. “This suggests they these regions may have lost some important binding sites that prevent them from acting as an enhancer.”

What it all boils down to in the end, Sackton said, is that birds have a limited number of options to pursue when it comes to the loss of flight, and so various species have gone to the same well again and again.

“That’s is the conclusion we would draw from this work,” he said. “There are a limited number of ways you can get this type of change in scaling, and they center on this regulation of early limb development.”

The study also highlights the power of the multi-disciplinary approach taken by Sackton, Edwards and colleagues.

“One of the things that was exciting about this project, for me personally, was how we were able bring the computational expertise in the Informatics Group to bear on this really important question in evolutionary biology. This joining of computational, statistical genetics with the natural history perspectives is important for getting the full picture of how these birds evolved.”

“It’s exciting what can be done with a research team with diverse skill sets,” Edwards added. “Our group had developmental biologists, computational biologists, morphologists, statisticians, population geneticists — and, of course, ornithologists. Each brings a different perspective and the results, I think, are amazing.”

This research was supported with funding from the National Science Foundation and the Natural Sciences and Engineering Research Council of Canada.

Horses hooves’ evolution, new research

This video is a 2017 National Geographic documentary about horse evolution.

From the University of Bristol in England:

Is one toe really better than three? How horse’ legs evolved for travel rather than speed

April 17, 2019

Palaeobiologists from the University of Bristol and Howard University (USA) have uncovered new evidence that suggests that horses’ legs have adapted over time to be optimised for endurance travel, rather than speed.

The ancestors of horses (including asses and zebras) had three toes on each foot. Because only single-toed (monodactyl) forms survive today this anatomy has been perceived as a superior evolutionary outcome, enabling horses to outrun predators.

But our interpretation of equine evolution may be biased by our own history with horses: performance at the racetrack has been less important for human history than the endurance of horses at slower speeds, and such endurance may have been the critical factor in horse evolution.

The research team combined evidence from the fossil record with existing studies on horse locomotion and propose that the adaptive significance of single-toed limbs was for trotting during roaming for food and water, rather than for galloping to avoid carnivores.

The real evolutionary ‘step forward’ in horse foot anatomy was not the loss of additional toes, but the evolution of the ‘spring foot’.

This pogo-stick type of foot anatomy evolved in the three-toed distant ancestors of modern horses, which sported an enlarged central toe but retained small ‘side toes’, which likely prevented the foot from over-extending during extreme locomotor performance.

The ‘spring foot’ enables the storage of elastic energy in the limb tendons during locomotion, and its evolution coincided with the spread of grasslands around 20 million years ago in North America (the original home of horse evolution).

The spring-footed horses radiated extensively and were as diverse during their time as antelopes in Africa today.

By around 11-million-years ago they also spread into Eurasia and Africa, where they eventually included forms larger than a modern horse. But only the lineage leading to modern horses, one amongst many, showed any tendency to reduce the number of toes.

If being single-toed was evolutionary advantageous, why did the majority of horses retain the three-toed condition for most of their evolutionary history?

Professor Christine Janis, lead author from the University of Bristol’s School of Earth Sciences (and also affiliated with Brown University, USA) said: “Early members of the single-toed horse lineage were not only losing their side toes, but the bones of the remaining central toe showed evidence of the boosting-up of the ‘spring foot’ apparatus, implying that these horses were becoming more reliant on energy-efficient locomotion.

“But at the same time these horses’ backs were becoming shorter and stiffer, contraindicative of adaptation for the back-flexing fast galloping gait. Rather, the preferred locomotion was more likely the medium-speed trot.”

The authors propose that the early single-toed horses were changing their daily foraging behaviour to roam more widely in search of food, promoting energy-saving adaptations in their feet.

The loss of the side toes may simply have been a consequence of upgrading the anatomy of the main, central toe, and with the boosted-up ligament system their original function was no longer necessary.

Single-toed horses appeared in North America around 12-million-years ago. Over the next few million years they radiated alongside three-toed horses but remained pony-sized and were neither diverse nor numerous.

But at this time the climate in northern latitudes was becoming cooler and drier. An increase in roaming behaviour would promote selection for the energy-efficient single-toed foot.

At the time, the foraging behaviour of the single-toed horses would have been one adaptive strategy among an equine diversity, much as different kinds of antelope have different modes of foraging today.

But by around five million years ago the cooling and drying trend became more intense worldwide; the former great diversity of three-toed horses had dwindled, and the direct ancestor of modern horses (early species of the genus Equus) appeared. By a million years ago all lineages of three-toed horses were extinct.

Why were single-toed horses the only equine lineage to survive to the present day? It is unlikely that competition was involved between the differently-adapted equines, as the Old World three-toed horses started their decline several million years before Equus emigrated from North America to join them 2.5 million years ago. More likely, the climatic changes of the late Cenozoic favoured the evolutionary strategy of the single-toed horses.

Professor Ray Bernor, the co-author of the paper, from Howard University’s College of Medicine, notes that the single-toed horses really just got a lucky break due to changing climates.

He added: “The three-toed horses, especially the Old World hipparions, were an incredibly successful radiation, and their skeletons showed adaptations for leaping and springing as well as running. But they evolved for a world that was warmer and wetter than that of today, and like many other large mammals did not survive to the present day.”

Single-toed horses became the dominant equines across the world in the past couple of million years, and only went extinct in the Americas at the end of the Pleistocene, around 12,000 years ago.

Professor Janis added: “However, nobody could have foreseen this eventual success ten million years ago, when single-toed horses were merely a minor lineage among equines, confined to North America.

“Their foot anatomy was ultimately important for finding food, rather than for avoiding becoming food themselves.”