Exploring the Interior

by Carl Strang

Now that the leaves are down from the trees and shrubs, I have been exploring the areas between the forest trails at St. James Farm Forest Preserve. Those areas are large enough that I cannot cover the forest adequately from the trails. I have found deer runs and old equestrian paths that will provide sufficient access for routine monitoring. Along the way I have found some interesting places. One foggy day I zig-zagged my way through part of the western forest.

This area has been cleared of invasive honeysuckles and other shrubs. Part of it is young second growth with a few clearings where perennial herbaceous plants are growing.

This area has been cleared of invasive honeysuckles and other shrubs. Part of it is young second growth with a few clearings where perennial herbaceous plants are growing.

Elsewhere there are old trees, many of them red oaks.

Elsewhere there are old trees, many of them red oaks.

Among the occasional boulders was this outwash-rounded fossiliferous one.

Among the occasional boulders was this outwash-rounded fossiliferous one.

The chunk of local Silurian dolomite appears to have been a spot on the ocean floor, adjacent to a reef, where there was a crinoid colony.

The chunk of local Silurian dolomite appears to have been a spot on the ocean floor, adjacent to a reef, where there was a crinoid colony.

A morainal depression held a huge fallen red oak.

A morainal depression held a huge fallen red oak.

The tree had lost the grip of most of its roots in the soil.

The last roots that were holding the tree up still show the relatively fresh color where they fractured.

The last roots that were holding the tree up still show the relatively fresh color where they fractured.

The orientation of the trunk relative to those broken roots suggests that a very strong wind from the west was the culprit.

 The oak didn’t go down alone. Broken stems reveal the trees it took out on either side. The force of the fall split the oak’s stem lengthwise.

The oak didn’t go down alone. Broken stems reveal the trees it took out on either side. The force of the fall split the oak’s stem lengthwise.

Each day in this exploration has brought its own delights.

Here, a beautiful moss colony became established on an old burn scar.

Here, a beautiful moss colony became established on an old burn scar.

One day when I was the preserve’s only human visitor, I saw one of St. James Farm’s coyotes. The fat belly and good coat indicate that this animal is a successful hunter.

One day when I was the preserve’s only human visitor, I saw one of St. James Farm’s coyotes. The fat belly and good coat indicate that this animal is a successful hunter.

So now the stage is set for routine coverage of St. James Farm’s ongoing natural history story.

 

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Literature Review: Human Evolution

by Carl Strang

Human. Photo by Linda Padera.

Human. Photo by Linda Padera.

Kimbel, William H., et al. 2014. Ardipithecus ramidus and the evolution of the human cranial base. Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1322639111  From a ScienceDaily article. The base of this skull of the 3.4-million-year-old species Ardipithecus ramidus places it in the Australopithecus-human line and separates it from chimpanzees and other apes. The shape features may reflect a change to a more upright posture, or the early reorganization of the brain. Earlier studies had indicated that Ardipithecus was arboreal but also could walk upright on the ground.

Ashton, N., et al. 2014. Hominin footprints from Early Pleistocene deposits at Happisburgh, UK. PLoS ONE 9(2): e88329. doi:10.1371/journal.pone.0088329 They describe footprints of hominins estimated to be 850,000 years old, in sediments of an age where flint tools have been found, and establishing the earliest evidence of hominins outside of Africa. A combination of pollen analysis and stratigraphy (e.g., the footprints are beneath glacial sediments) established the age.

Vernot, Benjamin, and Joshua M. Akey. 2014. Resurrecting surviving Neandertal lineages from modern human genomes. Science 343:1017-1021. Gibbons, Ann. 2014. Neandertals and moderns made imperfect mates. Science 343:471-472. The Gibbons article is a news review describing Vernot and Akey’s study, which showed that though Neandertals and modern humans interbred, there were costs to the hybridization. Only a small amount of Neandertal genetic material has persisted in Europeans and East Asians as a result, mainly genes connected with keratin function, and so affecting skin color, waterproofing, and resistance to cold, helping modern humans to survive in more northern latitudes. They looked at whole genomes of several hundred European and Asian people, and found that collectively they preserve about 20% of the Neanderthal genome (each individual has only 1-3%).

Huerta-Sánchez, Emilia, et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature, DOI: 10.1038/nature13408 From a ScienceDaily article. They looked at the genetics of these high altitude dwellers, and found that the main adaptation that allows them to live in low oxygen without heart problems comes from a gene their ancestors got through the Denisovans. The individuals who first moved into the area had some in their number descended from a modern human-Denisovan cross, and those people had a selective advantage in that environment.

Rasmussen, Morten, et al. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506 (7487): 225. DOI: 10.1038/nature13025 They worked up the genome of the only skeleton ever found in association with Clovis tools, that of a boy less than 2 years old found in a burial. His family and relatives are found to be ancestral to all Native Americans, and connected to Asian ancestors. The boy shares about 1/3 of his genes with the Baikal boy whose genome was sequenced in 2013, with the rest coming from east Asians, that blend happening before emigrating across the Bering Sea land bridge. The Clovis culture developed after the people were established in the New World, well before the 12,600-year age of the newly sequenced genome.

Literature Review: Pleistocene and Holocene

by Carl Strang

Today’s notes are from last year’s literature on the recent ice ages and subsequent prehistoric times. Some are biological in focus, others relevant to past and present climate change.

Coyotes once were bigger and more carnivorous than they are today, according to the following study.

Coyotes once were bigger and more carnivorous than they are today, according to the following study.

Meachen, J.A., A.C. Janowicz, J.E. Avery, and R.W. Sadleir. 2014. Ecological changes in coyotes (Canis latrans) in response to the ice age megafaunal extinctions. PLoS ONE 9(12): e116041. doi:10.1371/journal.pone.0116041 They measured coyote skulls from 29,000 years ago (La Brea tar pits) to present day, and found a transition from features associated with predation specialization to the present-day omnivory. Another study had found in addition a decrease in body size. They interpret this as a change in predator interactions. When the much larger dire wolf was the other dominant canid, and megafauna were abundant, coyotes could make a good living as specialist predators. Megafauna loss, and associated dire wolf extinction, opened the door for gray wolf immigration from Europe. This new, smaller predator was similar ecologically, but at the same time larger than the coyote, forcing a coyote niche shift to a more generalized diet.

Maher, K., and C.P. Chamberlain. 2014. Hydrologic regulation of chemical weathering and the geologic carbon cycle. Science 343:1502-1504. Kerr, Richard A. 2014. How Earth can cool without plunging into a deep freeze. Science 343:1189. The Kerr news article was based on the Maher and Chamberlain paper. The study looked at the mechanism that limits ice age cooling, preventing it from running away to a pole-to-pole glaciation. Volcanoes add carbon dioxide to the atmosphere, warming climate but also dissolving in rainwater, the resultant carbonic acid dissolving rock. The products flow to the sea, are taken up by plankton for skeleton building, and ultimately are buried. This removal process limits carbon dioxide buildup. Most of the dissolved rock is in mountains, and mountain uplift as in the Andes and Himalayas thus is tied to a global thermostat turndown. However, cooling slows the weathering reactions, allowing carbon dioxide to build back up.

Pena, Leopoldo D., and Steven L. Goldstein. 2014. Thermohaline circulation crisis and impacts during the mid-Pleistocene transition. Science 345:318-322. They found evidence for a profound change in oceanic circulation patterns corresponding to the change in glacial cycling from 41-thousand-year to 100-thousand-year durations. They conclude that “North Atlantic ice sheets reached a milestone in size and/or stability” that led to the ocean circulation change, resulting in a greater carbon dioxide drawdown, increased polar glaciation, and setting the pattern for the following 100,00-year cycles.

Guil-Guerrero, J.L., et al. 2014. The fat from frozen mammals reveals sources of essential fatty acids suitable for Paleolithic and Neolithic humans. PLoS ONE 9(1): e84480. doi:10.1371/journal.pone.0084480 They analyzed the fat chemistry of frozen woolly mammoths, horses and bison from Siberia. The fats were judged to be nutritionally good for human hunters of the time (41,000-4400 years ago). Furthermore, the fats of mammoths and horses were like those of hibernating mammals. The authors suggest that the mammoths and horses hibernated in similar fashion to present-day Yakutsk horses, which move little and mainly stand in sleeping positions during the coldest weather. The mammoth fatty acids suggest derivation from certain lichens in the diet.

Willerslev, Eske, et al. 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506 (7486): 47. DOI: 10.1038/nature12921 A large, multi-national team went into Pleistocene sediments and mummified gut contents, and used reference DNA from herbarium specimens to characterize vegetational changes over the past 50,000 years. They found that the last ice age caused a significant alteration of northern plant communities, greatly reducing forbs while increasing grasses and woody plants. Many of the megafauna herbivores such as woolly rhinoceros and woolly mammoth depended on the forbs for their protein content, and the authors believe that the failure of forb-rich communities to re-form after the ice receded contributed to or even caused megafaunal extinctions. No mention was made of human hunting in the ScienceDaily article describing the study.

Hoffecker, J. F., S. A. Elias, and D. H. O’Rourke. 2014. Out of Beringia? Science 343 (6174): 979. DOI: 10.1126/science.1250768 They reviewed cores taken from the Bering Sea and found that Beringia was not a barren grassland through the glacial times but had significant areas of tundra shrubs and trees. Animals including elk and moose likely lived there, and the likelihood of long-term human occupation seems good. This could provide a way that the ancestors of Native Americans could have been isolated from Asians for the 10,000 years, between 25,000 and 15,000 years ago, accounting for the genetic differences comparisons show. Beringia was not glaciated, and summers may well have been like those of today, though winters would have been severe. When the glaciers opened a way by melting, the 15,000-year Native American presence in the continent began as the Beringians moved in.

Literature Review: Paleogene Period

by Carl Strang

The dramatic departure of the Mesozoic Era and its dinosaurs (as well as a large proportion of other life forms) opened an immense volume of ecological space which was filled by mammals, birds and other diversifying descendants of the survivors. The following are notes from some of last year’s published studies of those early post-Mesozoic epochs.

Blonder, B., et al. 2014. Plant ecological strategies shift across the Cretaceous–Paleogene boundary. PLoS Biol 12(9): e1001949. doi:10.1371/journal.pbio.1001949

Chase, J.M. 2014. A plant’s guide to surviving the Chicxulub impact. PLoS Biol 12(9): e1001948. doi:10.1371/journal.pbio.1001948 This study (interpreted in the Chase paper) found that slow-growing evergreen plants were selected against by the “impact winter” effects of the end-Cretaceous impact event. Plant species with faster growth, cheaper expendable leaves, and thus a quick response to changing and fluctuating conditions, had an advantage and better survival.

The following study suggests that all leaf miners, at least in half the continent, went extinct with the end of the Cretaceous. And yes, that is a poison ivy leaf with 4 leaflets.

The following study suggests that all leaf miners, at least in half the continent, went extinct with the end of the Cretaceous. And yes, that is a poison ivy leaf with 4 leaflets.

Carvalho, Mónica R., et al. 2014. Insect leaf-chewing damage tracks herbivore richness in modern and ancient forests. PLoS ONE 9 (5): e94950. DOI: 10.1371/journal.pone.0094950  They looked at fossil leaf mines, and concluded that all miners went extinct in western North America with the end of the Cretaceous. Newly evolved leaf mining species appeared within 1 million years.

Wilf, Peter, and Ignacio H. Escapa. 2014. Green web or megabiased clock? Plant fossils from Gondwanan Patagonia speak on evolutionary radiations. New Phytologist DOI: 10.1111/nph.13114 They examined a new array of plant fossils and found them to be significantly older than molecular clock studies had indicated they would be. This result points to a need to reconsider molecular dating. It also supports the idea that plants dispersed among the southern continents by continental drift more than by rafting, which had been supported by the younger ages of evolutionary diversification suggested by the molecular dating.

Solé, F., et al. 2014. Dental and tarsal anatomy of ‘miacis’ Latouri and a phylogenetic analysis of the earliest carnivoraforms (mammalia, Carnivoramorpha). Journal of Vertebrate Paleontology, 34(1): 1-21. As described in a ScienceDaily article. They studied fossils (teeth and ankle bones) of a European mammal, Dormaalcyon latouri, from the early Eocene of Belgium, and concluded it is a basal carnivore. It appears to have been arboreal, which implies a continuous forest connecting Eurasia with North America at the time which provided a corridor for carnivore immigration to North America (the age and location suggests that carnivores first evolved in Europe). At the same time it is derived enough to imply that there were early carnivores in the late Paleocene as well.

Rose, Kenneth D., et al. 2014. Early Eocene fossils suggest that the mammalian order Perissodactyla originated in India. Nature Communications 5: 5570 DOI: 10.1038/ncomms6570 As described in a ScienceDaily article. They found fossils bridging Perissodactyla with earlier mammalian groups, from around 56 million years ago, when India still was an island drifting toward Asia. This suggests that the group originated there during that period of isolation. It has been speculated that primates likewise started there, though that has yet to be determined.

Mayr, G., and V. Wilde. 2014. Eocene fossil is earliest evidence of flower-visiting by birds. Biology Letters 10 (5): 20140223. DOI: 10.1098/rsbl.2014.0223 As described in a ScienceDaily article. They describe a 47-million-year-old fossil bird with stomach contents dominated by diverse pollens, and with anatomy consistent with nectar feeding, and conclude that this is the oldest known bird species that visited flowers.

Literature Review: Bird Evolution

by Carl Strang

As I mentioned last week, the Mesozoic Era is a perennial hot topic in paleontological research. Lately, a hot topic within that hot topic has been the evolution of birds (plus the lead-up to the first birds in the feathered dinosaurs, some studies of which were included in last week’s listing). Here are notes from some studies published last year.

Dinosaur descendant

Dinosaur descendant

Mitchell, Jonathan H., and Peter J. Makovicky. 2014. Low ecological disparity in early Cretaceous birds. Proceedings of the Royal Society B, DOI: 10.1098/rspb.2014.0608 As described in a ScienceDaily article. They did an intensive study of a collection of fossil birds from China, early in the Cretaceous Period around 125 million years ago, when birds were a relatively new addition to the fauna. They concluded that the collection probably is a reasonably good approximation of what was there, and that it shows a remarkable lack of diversity. The size range and dietary breadth were limited, and large birds and water birds were missing. Most birds were sparrow to crow sized. There were some differences from today, as some species retained teeth or bony tails. Indications are that they lived in the forest and on the ground, and ate mostly insects and seeds. Though some of this limitation might have resulted from competition with established groups such as pterosaurs, the authors point to the lack of time for evolutionary diversification to occur as the main constraint.

Brusatte, Stephen L., Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell. 2014. Gradual assembly of avian body plan culminated in rapid rates of evolution across the dinosaur-bird transition. Current Biology, DOI: 10.1016/j.cub.2014.08.034 As described in a ScienceDaily article. They looked at the evolutionary development of various structural components of birds, such as feathers, wishbone and wings. The elements of the bird body appeared separately over a very long period of time in the fossil record, with a slow convergence on the ultimate bird body plan in the line of theropod dinosaurs that led to them. Thus there is no stepwise appearance of the first bird. However, once the first birds had evolved, their diversification and continued evolution happened much more rapidly, demonstrating the advantages of that body plan.

Puttick, Mark N., Gavin H. Thomas, and Michael J. Benton. 2014. High rates of evolution preceded the origin of birds. Evolution, DOI: 10.1111/evo.12363 As described in a ScienceDaily article. They looked at the fossil record and used computer models to calculate rates of evolution of various traits. Two features essential to birds, small size and elongated forelimbs, began to appear 20 million years prior to Archaeopteryx, so that there were many species of small feathered dinosaurs (paraves) capable of flight well before the first birds appeared.

Meredith, R.W., G. Zhang, M. T. P. Gilbert, E. D. Jarvis, and M. S. Springer. 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346 (6215): 1254390 DOI: 10.1126/science.1254390 This portion of the whole-genome bird comparison study found that all modern birds point to a single common ancestor that lost the capability to grow teeth more than 100 million years ago, over a short span of time developing mutations inactivating 6 genes involved in enamel and dentin formation.

Lee, Michael S.Y., Andrea Cau, Darren Naish, and Gareth J. Dyke. 2014. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds. Science 345:562-566. They did a detailed statistical study across the entire range (time and taxonomic) of theropod dinosaurs, and found a trend over the Mesozoic of reduction in body mass, culminating in the birds. This set the stage for other skeletal modifications that made birds possible.

Literature Review: Mesozoic Era

by Carl Strang

As always, fascination with dinosaurs in particular produced plenty of interesting new Mesozoic Era studies published in 2014. Those focused on the evolution of birds will follow next week.

Dinosaurs weren’t the only Mesozoic life forms, but they certainly are the first to come to mind.

Dinosaurs weren’t the only Mesozoic life forms, but they certainly are the first to come to mind.

Grady, John M., et al. 2014. Evidence for mesothermy in dinosaurs. Science 344:1268-1272. They looked at growth rates as indicated by bone rings, comparing such data to present-day ectotherms, endotherms and mesotherms such as certain sharks, tuna, sea turtles and echidnas. They found that the dinosaurs fit with that last group. Given the climatic warmth of the Mesozoic, this is a feasible result, giving them an advantage over slower ectotherms without the higher energy demands of endotherms.

Motani, Ryosuke, et al. 2014. A basal ichthyosauriform with a short snout from the Lower Triassic of China. Nature, DOI: 10.1038/nature13866 This fossil, Cartorhynchus lenticarpus, from 4 million years post-Permian mass extinction, fills the gap between terrestrial reptiles and marine ichthyosaurs. The 16-inch-long animal had flippers but strong wrists, a short snout, and heavy bone structure. It is regarded as an amphibious reptile that lived in coastal China, the heavy bones having been predicted as necessary for withstanding wave forces.

Koschowitz, Marie-Claire, Christian Fischer, and Martin Sander. 2014. Beyond the rainbow. Science 346:416-419. They review recent literature and paint a picture of dinosaurs first evolving proto-feathers as insulation, facilitating their new capacity for greater metabolism. This was especially important in the theropod lineage that ultimately led to birds, as body size decreased over time. Such a covering would have hidden the skin’s structural color, however, taking away any prismatic or reflective production of iridescence, blues, greens, and ultraviolets, and losing them as a signal. That loss provided a selective advantage to vaned feathers, which recovered the structural color capability. The vaned feather in turn provided the foundation, eventually, for flight. These steps are dependent upon the dinosaurs’ color vision, which they share with a broad range of reptiles.

Godefroit, P., et al. 2014. A Jurassic ornithischian dinosaur from Siberia with both feathers and scales. Science 345:451-455. Kulindadromeus zabaikalicus was found in a new site in Siberia. It is a basal ornithiscian that had filamented feathers, for the first time proving these were not limited to the theropods (earlier, fossil ornithiscians have been found with bristle-like feathers). Filamented ones were found on the limbs, and the rest of the body was largely covered in bristle-like feathers. The tail and lower legs were scaled. This dinosaur was around 1m long.

Button, D. J., E. J. Rayfield, and P. M. Barrett. 2014. Cranial biomechanics underpins high sauropod diversity in resource-poor environments. Proceedings of the Royal Society B: Biological Sciences 281 (1795): 20142114. DOI: 10.1098/rspb.2014.2114 They reconstructed the anatomy of coexisting sauropods, Camarasaurus and Diplodocus, to get an idea of how two such enormous animals could coexist in an arid, relatively plant-poor, environment. Camarasaurus had a strong bite, and could handle tougher vegetation such as woody plants. Diplodocus had a weaker bite but stronger neck, so it would have had an easier time pulling out and handling softer plants like ferns.

Geological Society of America. 2014. “Kung fu stegosaur: Lethal fighters when necessary.” ScienceDaily, <www.sciencedaily.com/releases/2014/10/141021114903.htm>. Robert Bakker and colleagues described an allosaur pubis bone which developed an infection following a wound from a stegosaur tail spike. The infection probably killed the predator. The wound is an indication of an accurate defensive tail swing by the stegosaur.

Grossi, B., et al. 2014. Walking like dinosaurs: chickens with artificial tails provide clues about non-avian theropod locomotion. PLoS ONE 9(2): e88458. doi:10.1371/journal.pone.0088458 They raised chickens with artificial tails attached, to see if this change in center of mass would change their locomotion to match that theorized for theropods. The experiment was successful, producing birds that moved more through use of femoral movement rather than the more crouched, knee focused gait of birds.

Andrew A. Farke, W. Desmond Maxwell, Richard L. Cifelli, Mathew J. Wedel. 2014. A ceratopsian dinosaur from the Lower Cretaceous of western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055  They describe the earliest known North American ceratopsian, a crow-sized dinosaur similar to contemporary similar Asian species, providing evidence for a connection between the continents around that time. Montana is the location of the find.

Ibrahim, Nizar, et al. 2014. Semiaquatic adaptations in a giant predatory dinosaur. Science 345:1613-1616. They describe a partial skeleton of Spinosaurus aegyptiacus from Morocco. It shows several adaptations for a semiaquatic lifestyle, including nostrils brought back to the midpoint of the skull; an elongate neck and trunk that shift the center of mass forward; a downsized pelvic girdle; short limbs; solid limb bones (helpful to counter buoyancy when swimming); and muscle attachment indicators and flat-bottomed claws on the hind feet “consistent with aquatic foot-propelled locomotion.” The long rays on the dorsal spine “may have been enveloped in skin that functioned primarily for display on land and in water.” Its age is estimated at 97 million years. The elongate toothy snout may indicate this was largely a fish predator. It was found in river sediments, in a river system where there were common sharks, sawfish, coelacanths, lungfish and others.

Krause, David W., et al. 2014. First cranial remains of a gondwanatherian mammal reveal remarkable mosaicism. Nature, DOI: 10.1038/nature13922 As described in a ScienceDaily article. This describes the unprecedented find of a complete skull from Madagascar, a 20-pound mammal contemporary with the latest dinosaurs, and by far the largest southern continent mammal from the Mesozoic (this is only the third Cretaceous mammal skull from the entire southern hemisphere). Vintana sertichi was a gondwanatherian, a southern hemisphere group previously known only from a few teeth. It appears to have been a nocturnal herbivore, with very large eye sockets and anchors for strong chewing muscles. The details of the skull show that this group is close to the multituberculates and another odd group, the Haramiyida.

Literature Review: Paleozoic Era

by Carl Strang

The first animals which unambiguously connect to present day forms appear in the fossil record early in the Paleozoic Era, which began 542 million years ago, billions of years after the planet first formed. Here are some notes from studies of this era published in 2014.

American alligator. One of the following studies places the split between the reptilian crocodile-dinosaur-bird group and the lizard-snake group at the very end of the Paleozoic Era.

American alligator. One of the following studies places the split between the reptilian crocodile-dinosaur-bird group and the lizard-snake group at the very end of the Paleozoic Era.

Cong, Peiyun, et al. 2014. Brain structure resolves the segmental affinity of anomalocaridid appendages. Nature, DOI: 10.1038/nature13486 They studied the brain structure of Lyrarapax unguispinus, a fossilized relative of Anomalocaris, and found it was both simpler than those of its contemporary prey, and very similar to those of today’s onychophorans, or velvet worms, terrestrial southern hemisphere forest floor predators with unusual antennae that connect to the brain in the same way that the pair of grasping appendages connected to the brain of Lyrarapax. The similarities suggest a common ancestry.

Jourdan, F., et al. 2014. High-precision dating of the Kalkarindji large igneous province, Australia, and synchrony with the Early-Middle Cambrian (Stage 4-5) extinction. Geology 42 (6): 543. DOI: 10.1130/G35434.1 From a ScienceDaily article. The first major extinction event, which took out 50% of species in the Middle Cambrian, was caused by a mass volcanic eruption in Australia according to this study.

Morris, Simon Conway, and Jean-Bernard Caron. 2014. A primitive fish from the Cambrian of North America. Nature, DOI: 10.1038/nature13414 New Burgess shale fossils from the Cambrian of 505mya (million years ago) show detail in one of the earliest fishes, Metaspriggina, in which branchial arches are revealed as paired, with the first pair slightly thicker than the others (a step toward the first jaw). They had large eyes, and probably were good swimmers.

Shubin, Neil H., Edward B. Daeschler, and Farish A. Jenkins, Jr. 2014. Pelvic girdle and fin of Tiktaalik roseae. PNAS, DOI: 10.1073/pnas.1322559111 From a ScienceDaily article. They describe the anatomy of the rear part of this fish, previously known only from anterior portions. This animal was transitional toward terrestrial life, living in a delta environment where the ability to cross over land from stream to stream was advantageous. It was large, as much as 9 feet long, with large teeth making it somewhat reminiscent of a crocodile. It was lobe-finned, had a flexible neck, and rudimentary lungs. Its well-developed shoulder girdle previously was known, but it had been assumed that it crawled with only its front fins. The surprise was that the pelvic girdle also is developed, with a ball and socket joint and strong hind fins, so these fish had rudiments of four, rather than just two legs.

Ezcurra, M.D., T.M. Scheyer, and R.J. Butler. 2014. The origin and early evolution of Sauria: reassessing the Permian saurian fossil record and the timing of the crocodile-lizard divergence. PLoS ONE 9(2): e89165. doi:10.1371/journal.pone.0089165 They took a close look at Permian fossils in an attempt to resolve debate on when the split happened between the reptilian line leading to crocodiles, dinosaurs and birds on the one hand (archosauromorphs) and lizards and snakes on the other (lepidosauromorphs). They concluded that only the former have been found in the Permian, and place the earliest possible time for the split at 254.7 million years ago (very late Permian).

Literature Review: Proterozoic Eon

by Carl Strang

The Proterozoic Eon spanned the immense period of time from 2.5 billion to 542 million years ago. It has captured the imaginations of many researchers, because its rocks have teased them with clues that hint at amazing stories, such as the first eukaryotic life forms, a billion-year stall-out of life’s evolution, a globe-covering ice age (“snowball Earth”), and the first appearance of multicellular organisms, which may or may not be connected to those we have today. Here are my notes from last year on some studies of that eon.

There was no terrestrial life in the Proterozoic, but this was the time when the Chicago region’s crust joined the North American continent, appending itself to the southern boundary of the Canadian Shield.

There was no terrestrial life in the Proterozoic, but this was the time when the Chicago region’s crust joined the North American continent, appending itself to the southern boundary of the Canadian Shield.

Northwestern University. 2014. “Mysterious Midcontinent Rift is a geological hybrid.” ScienceDaily, <www.sciencedaily.com/releases/2014/10/141016132850.htm>. This article described a collaborative project, still unpublished, focusing on the mid-continent rift that left Lake Superior as its most visible feature. The rift was underway in the mid-Proterozoic when it filled with magma and stopped opening. More magma subsequently poured out on top of it, pushing the original body down and thickening the crust there. The feature thus combines rift characteristics with those of a large igneous province, and contains more volcanic rock than any other mid-continent rift on the planet. Incidentally the pieces of volcanic rock we find in local glacial drift came from that source.

Sánchez-Baracaldo, Patricia, Andy Ridgwell, and John A. Raven. 2014. A Neoproterozoic transition in the marine nitrogen cycle. Current Biology, DOI: 10.1016/j.cub.2014.01.041  From a ScienceDaily article. They used molecular clock estimation to place the appearance of nitrogen fixing by cyanobacteria at 800 million years ago. This may have removed the nutrient limitation that was holding life back, setting the stage for proliferation both of biomass and of evolutionary potential. However, this timing also is just before the Snowball Earth glaciation event, and the authors suspect that the algal bloom might have sequestered enough carbon to be a trigger for that event.

Hoyal Cuthill, Jennifer F., and Simon Conway Morris. 2014. Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan. PNAS, DOI: 10.1073/pnas.1408542111  From a ScienceDaily article. They looked at the 3-dimensional structure of Ediacaran life forms (referred to as rangeomorphs), and found that their fractal designs efficiently filled the space around them. They argue that these were animals, living too deep in the sea for photosynthesis, which absorbed dissolved nutrients directly from the water. This was possible until predators, filter feeders and more mobile life forms rendered this subsistence style unsupportable.

Liu, Alex, et al. 2014. Haootia quadriformis n. gen., n. sp., interpreted as muscular Cnidarian impression from the Late Ediacaran period (approx. 560 Ma). Proceedings of the Royal Society B, DOI: 10.1098/rspb.2014.1202  From a ScienceDaily article. They described an Ediacaran fossil from Newfoundland, 560 million years old, concluding that it was a cnidarian with muscle tissue, the earliest animal with muscle.

Literature Review: Hadean and Archean Eons

by Carl Strang

Today’s post begins a series of weekly updates from last year’s literature on prehistoric life and the associated geology. In this one I include selected studies of our planet’s first two eons, covering the first 2 billion years (out of 4.6 total) of the Earth’s existence. The Hadean Eon is defined by the lack of surviving crust. It is known mainly from moon rocks, which along with certain deep-Earth data have told of a collision between the early Earth and a Mars-sized object named Theia. The moon was a product of that collision. The following Archean Eon brought the first-formed planetary crust, oceans, and the origin of life.

Hadean Eon

Arpita, Roy, et al. 2014. Earthshine on a young moon: explaining the lunar farside highlands. Astrophysical Journal Letters, DOI: 10.1088/2041-8205/788/2/L42 The far side of the moon has hardly any maria, unlike the familiar near side which has large areas covered by those ancient lava flows. This paper provides an explanation as to why the far side crust is so much thicker, so that meteor strikes did not so readily punch through. It is built on the collision that formed the moon. Both Earth and moon were much closer together at first, and the moon became tidally locked, so that the one side always faced the Earth. The heat of the Earth kept the near side hotter and molten longer, so that aluminum and calcium compounds cooled sooner and fell out more thickly on the far side, ultimately combining with silicates to form a thicker, feldspar-rich crust there.

Herwartz, D., A. Pack, B. Friedrichs, and A. Bischoff. 2014. Identification of the giant impactor Theia in lunar rocks. Science 344 (6188): 1146-1150. Data casting doubt on the Theia collision hypothesis were based on lunar rocks that had been contaminated through contact with Earth. New measurements taken from samples returned by NASA missions from the moon confirm that the proportion of Earth material in the moon is low enough to fit collision models.

Valley, John W., et al. 2014. Hadean age for a post-magma-ocean zircon confirmed by atom-probe tomography. Nature Geoscience, DOI: 10.1038/ngeo2075  They found zircon crystals in certain Australian rocks that formed 4.4 billion years ago, pushing back the earliest crust formation time and potentially permitting the formation of life earlier than had been thought. They suggest a hydrosphere may have existed as soon as 100 million years after the Theia collision.

Stromatolite fossil, Kakabeka Falls Provincial Park, Ontario. Stromatolites were colonial photosynthetic bacteria, responsible for the initial buildup of oxygen in the Archean atmosphere.

Stromatolite fossil, Kakabeka Falls Provincial Park, Ontario. Stromatolites were colonial photosynthetic bacteria, responsible for the initial buildup of oxygen in the Archean atmosphere.

Archean Eon

Russell, Michael J., et al. 2014. The drive to life on wet and icy worlds. Astrobiology 14 (4): 308. DOI: 10.1089/ast.2013.1110  From a ScienceDaily article. They are examining one way life could make a start, around alkaline thermal vents at the bottom of an otherwise acidic (carbon dioxide rich) ocean. “Life takes advantage of unbalanced states on the planet, which may have been the case billions of years ago at the alkaline hydrothermal vents,” said Russell. “Life is the process that resolves these disequilibria.” The article describes two possible geological analogs to processes that go on in mitochondria. One imbalance is in protons, or hydrogen ions, which would have been more concentrated on the outsides of vent chimneys. The other would be the gradient from the methane and hydrogen in the vent to carbon dioxide in the surrounding ocean, which could have produced an electron transfer. The mineral analogs to enzymes are thought to have been “green rust” (not further identified in the article; its participation could have stored energy from the proton imbalance in a phosphate-containing molecule) and molybdenum (known to transfer two electrons at a time in physiological processes). They point out that these are processes that could be common on other watery planets.

Martin, William F., Filipa L. Sousa, and Nick Lane. 2014. Energy at life’s origin. Science 344:1092-1093. They compare the energy-releasing chemical reactions common to living things and find them to be similar to those going on at alkaline hydrothermal vents, suggesting that such places were where life began.

Literature Review: Evo-Devo

by Carl Strang

One of the most fascinating biological disciplines to emerge in recent years is evo-devo, the study of the genetic regulation of embryological development, with the goal of understanding the role of evolution. Most of the work to date has been done in animals, and the connections between distantly related species often are amazing, as several studies cited below reveal. Plants are increasingly subjects of this form of study, and the general patterns often prove to be similar to those in animals, as illustrated in the Vlad et al. study. Humans don’t escape this type of scrutiny, and we prove to have very similar vocal controls to those of songbirds. Fossil studies often are brought into these researches, as shown in the studies of breathing in turtles and the evolutionary relationships of daddy longlegs (harvestmen). Even the electric organs of various groups of fishes are subject to this kind of analysis.

The first study goes into the development of leaves, which in some species results in their division into separate leaflets as in this buckeye leaf.

The first study goes into the development of leaves, which in some species results in their division into separate leaflets as in this buckeye leaf.

Vlad, Daniela, et al. 2014. Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science 343:780-783. They looked at developmental regulation of leaflet formation. A particular protein produced through homeobox activity represses growth in areas that end up being between leaflets. The associated gene evolved within a duplicated section of DNA. They found a species in which the duplicate was lost, resulting in simple leaves.

Pfenning, Andreas R., et al. 2014. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science 346:1333. They studied genomes of a variety of birds and primates, and found that song-learning birds and humans share genes that produce connections between their brains and vocal apparatus, genes that are inactive in bird and primate groups that do not sing or speak. Thus brain structure and circuitry features associated with song learning in birds and vocal learning in humans are analogous and similar, and homologous at the level of brain regions. Genetic underpinnings for these structures likewise are similar. “The finding that convergent neural circuits for vocal learning are accompanied by convergent molecular changes of multiple genes in species separated my millions of years from a common ancestor indicates that brain circuits for complex traits may have limited ways in which they could have evolved from that ancestor.”

Lyson, Tyler R., et al. 2014. Origin of the unique ventilatory apparatus of turtles. Nature Communications 5: 5211. DOI: 10.1038/ncomms6211  Described in ScienceDaily. They did a detailed study of modern and fossil turtles, focusing on breathing, because turtles are the only air-breathing vertebrates that cannot employ the ribs. Turtles breathe with a ring of muscles surrounding the lungs. This system was in place in the early (260mya, Permian Period) African turtle Eunotosaurus africanus. They found that the system evolved gradually, the body wall stiffening as ribs broadened (for reasons still to be determined), and the musculature gradually developing to take more and more of the load.

Gallant, J. R., et al. 2014. Genomic basis for the convergent evolution of electric organs. Science 344:1522-1525. They studied the genetic and developmental aspects of electric fishes, 6 separate groups of which independently evolved the ability to produce electricity. They found that the same genetic basis and developmental pathway evolved to the same endpoint in all these different lines. Certain muscle cells lost their contraction ability and increased their membrane’s ability to manipulate ions and build up charge. They are set up in series down the length of the fish, increasing the voltage. The most powerful is the Amazon’s electric “eel” (more like a catfish), which one of the researchers characterized as “in essence a frog with a built-in five-and-a-half-foot cattle prod.” These fishes all live in murky waters, and use their electric capability to sense their surroundings, communicate, stun prey, and defend themselves.

Nuño de la Rosa, Laura, Gerd B. Müller, and Brian D. Metscher. 2014. The lateral mesodermal divide: an epigenetic model of the origin of paired fins. Evolution & Development 16 (1): 38. DOI: 10.1111/ede.12061  From a ScienceDaily article. They looked at the fossil record and the genetics of development, and found that the body cavity prohibits development of limbs in the region of body axis where it occurs. The result is a single pair of limbs in front, and a single pair behind that region.

Garwood, Russell J., Prashant P. Sharma, Jason A. Dunlop, and Gonzalo Giribet. 2014. A Paleozoic stem group to mite harvestmen revealed through integration of phylogenetics and development. Current Biology, DOI: 10.1016/j.cub.2014.03.039  From a ScienceDaily article. They studied a rare early harvestman fossil with x-ray scanning which provided unusual 3D detail. The fossil was 305 million years old (Pennsylvanian Period), from France. It showed an extra pair of eyes, set laterally, which subsequent study revealed appear in vestigial form at a point in embryo development (mature present-day harvestmen have only a single pair of eyes). The authors mentioned that harvestmen are more closely related to scorpions than to spiders.

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