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: 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, <>. 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, <>. 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: Human Evolution

by Carl Strang

At some point, paleontological studies come back to our own ancestry. Here are my notes on some studies published last year.



Schmid, P., et al. 2013. Mosaic Morphology in the Thorax of Australopithecus sediba. Science 340:164-165. Irish, J. D., et al. 2013. Dental Morphology and the Phylogenetic “Place” of Australopithecus sediba. Science 340:164. These are two of a series of studies of this hominin reported in this issue. They studied skeletal portions of a single specimen from South Africa of 2 million years ago. It proves to be a mosaic of primitive and modern human features, so they conclude it is an ancestor or early form of Homo, closer to our genus and to Australopithecus africanus than is the east African Australopithecus afarensis. The structure of the arms, shoulder blades, and the narrow upper ribcage suggest this was a tree climbing species that could not run for long distances. At the same time it had the narrow waist of a human. The feet turned sharply inwards, distinguishing it from other Australopithecines. The structure of the teeth was a major line of evidence indicating the connections between sediba and Homo.

Lordkipanidze, D., et al. 2013. A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo. Science 342:326-331. They have studied several skulls from European Georgia that provide data on individual variation of Homo erectus. It seems likely that fewer Homo species existed than had been thought, and that erectus evolved about 2 million years ago and then (alone) spread out of Africa, eventually reaching Asia 1.2 million years ago.

Meyer, Matthias, et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 2013; DOI: 10.1038/nature12788  From a ScienceDaily article. They sequenced mitochondrial DNA from bones recovered in a cave in northern Spain. The bones, 400,000 years old, were revealed to have connections to the Denisovans, previously known only from Asia. The common ancestor between these Homo heidelbergensis bones and the Denisovans was estimated to live 700,000 years ago. The connection could reflect an ancestral split between genetic lines, or an inflow of Denisovan genes through population movements.

Rito, T, et al. 2013. The first modern human dispersals across Africa. PLoS ONE 8(11): e80031. doi:10.1371/journal.pone.0080031  Their analysis using updated technology points to the “mitochondrial Eve” in central Africa 180,000 years ago, a time of low population density. There then was a separation by 130,000 years ago between some groups that have remained in extreme southern Africa, and others in central and east Africa who became the ancestors of all modern humans. Subsequent dispersal episodes correspond to, and may have been stimulated by, a series of droughts 135,000-75,000 years ago.

Prüfer, Kay, et al. 2013. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature DOI: 10.1038/nature12886  From a ScienceDaily article. They developed a complete Neanderthal genome from 50,000 years ago, and comparisons to the genomes of modern humans and Denisovans reveals a complex pattern of occasional interbreeding. Neanderthals and Denisovans prove to be very closely related, the split between them estimated at 300,000 years ago. Their common ancestor population split from the modern human line 400,000 years ago. 1.5-2.1% of non-African modern human genetics comes from later interbreeding with Neanderthals. Denisovans also contributed small portions of genes to Asian and Oceanic modern humans, the largest an estimated 6% in Australian aboriginals, New Guineans, and some Pacific islanders. Asians and Native Americans have a portion of 0.2%. The Denisovans also are found to have interbred with an unknown fourth group, possibly Homo erectus, that had split from all the others a million years ago. The genetics suggest that Neanderthal and Denisovan groups were small, and inbreeding was relatively common.

Raghavan, Maanasa, et al. 2013. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature DOI: 10.1038/nature12736  From a ScienceDaily article. The DNA of a Siberian boy of 24,000 years ago shows elements connecting his ancestry to various parts of Asia, and also to Europe. It also has enough in common with Native American DNA to place the boy’s population as ancestral to Native Americans. Those Siberians were part of a widely wandering Eurasian people in the Ice Age, who naturally would have extended the wandering across the Bering Sea when glaciers drew it down to provide the land connection to North America.

Battaglia, V, et al. 2013. The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390  They found that Central  and South American Native Americans are connected to ancestors in southern Siberia as well as to North Americans. The results support two waves of immigration from North America, one reaching Mexico and a later one rapidly populating areas farther south.

Bollongino, Ruth, et al. 2013. 2000 Years of Parallel Societies in Stone Age Central Europe. Science DOI: 10.1126/science.1245049  From ScienceDaily article. People in Europe all were hunter-gatherers until 7500 years ago (modern humans arrived there 45,000 years ago, survived the ice age, and warming began 10,000 years ago). Immigrants brought agriculture from the south around 7500 years ago, and this study found that the hunter-gatherers persisted in that culture alongside the agriculturists for 2500 years before switching to agriculture themselves. The two societies lived side by side and buried their dead in the same cave. Genetic and chemical studies indicate that hunter-gatherer women sometimes married into the agriculturists, but not the reverse.

Pugach, Irina, et al. Genome-wide data substantiates Holocene gene flow from India to Australia. PNAS, January 14, 2013 DOI: 10.1073/pnas.1211927110  They found that Australian aboriginals, who were established in that continent by 45,000 years ago, were not isolated for all of that time. Their genetics indicate that around 4000 years ago there was immigration (“substantial gene flow”) from India. That timing coincides with the arrival of the dingo, and changes in plant processing and stone tool technologies.

Literature Review: Ice Ages and Climate

by Carl Strang

Today’s literature focus is on two studies from last year that increased our understanding of ice age dynamics and how our changes to the atmosphere may alter them.

Kokechik Bay, Alaska, late winter

Kokechik Bay, Alaska, late winter

Ballantyne, Ashley P., et al. 2013. The amplification of Arctic terrestrial surface temperatures by reduced sea-ice extent during the Pliocene. Palaeogeography, Palaeoclimatology, Palaeoecology, DOI: 10.1016/j.palaeo.2013.05.002  As described in a ScienceDaily article. Recent measures of carbon dioxide in the atmosphere have brought current levels into the range of the Pliocene, which was 3.5-9 degrees F warmer than today. A modeling study indicates that the difference may have been that the Arctic Ocean then was open year-round, a condition toward which we are trending now.

Kerr, Richard A. 2013. How to make a great ice age, again and again and again. Science 341:599. News article describing a study published in Nature that reports an advance in understanding the continental glacier cycle. That cycle corresponds to the 100,000-year stretching and shrinking of the Earth’s orbit around the sun, but that’s too weak to account for ice building and declining. The group led by Ayako Abe-Ouchi modeled in the 23,000-year wobble in the Earth’s spin axis, plus global climate modeling and data on northern ice sheets, which involve changing carbon dioxide levels and the mass of the ice. Simulated ice sheets expanded and contracted in close to the actual pattern. Ice gradually builds over the 100,000-year cycle, but then the 23,000-year cycle corresponds to the warming phase of the longer one, adding summer warmth. By then, crustal depression by the ice mass means that the ice is at a lower, warmer altitude (1 km of depression), and the glacier rapidly melts.

Literature Review: Sabertooth Studies

by Carl Strang

Saber-toothed predators have evolved in several mammalian families. A couple interesting studies of them appeared last year in the journals I follow.

Steven C. Wallace, Richard C. Hulbert. 2013. A new machairodont from the Palmetto Fauna (Early Pliocene) of Florida, with comments on the origin of the Smilodontini (Mammalia, Carnivora, Felidae). PLoS ONE,; 8 (3): e56173 DOI: 10.1371/journal.pone.0056173  They describe Rhizosmilodon fiteae, a 5 million year old ancestor of the sabertooth cat Smilodon, from Florida, and conclude that Smilodon (which first appeared in the fossil record 2.5 million years ago) evolved in North America.

Meachen-Samuels, Julie A. 2012. Morphological convergence of the prey-killing arsenal of sabertooth predators. Paleobiology 38:1-14. She looked for correlations between saber tooth and forelimb morphology in nimravids (late Eocene-early Miocene), Barbourofelis (late Miocene), and sabertooth cats (late Miocene-Pleistocene). Felids are thought to have replaced nimravids in the “sabertooth niche.” The saber teeth have dirk-tooth forms (very elongated, laterally compressed, serrations fine or absent) and scimitar-tooth forms (less elongated, less compressed, often coarsely serrated). Dirk-toothed species have been thought to be ambush predators with more robust limbs, scimitar-tooth forms more cursorial with lighter limbs suitable for running down prey. Some, in the felid genus Xenosmilus, combined scimitar teeth with robust limbs, however. Present day large cats have strong limbs for holding prey, and kill with choke-hold bites that require round or conical, short canines for strength. Saber canines are more fragile, and unsuitable for choke holds. Saber toothed species generally proved to be more robust than the present-day conical toothed species, with larger muscle attachment points, and also had wider paws. This was especially true of nimravids, which are thought to have been tree climbers. Dirk-toothed species were somewhat more robust than scimitar species. There are several known co-occurrences of conical, dirk and scimitar species, including locations in California, Idaho and Florida. Prey apparently were subdued with the strong forelimbs, then killed with the saber teeth. Meachen-Samuels suggests that some nimravids were tree climbers, but most sabertooth species were not, an additional support being their short tails (long tails are associated with tree climbing in many present day species).

I don’t have a sabertooth photo, but the final paper applies broadly to extinct animals including mastodons.

I don’t have a sabertooth photo, but the final paper applies broadly to extinct animals including mastodons.

Sherkow, Jacob S., and Henry T. Greely. 2013. What if extinction is not forever? Science 340:32-33. In this review article the authors summarize possibilities, technical challenges and ethical considerations for bringing back extinct species through methods including back-breeding (where surviving species contain among them the genome of an extinct relative), cloning (using genetic material from museum specimens, for instance nuclei from somatic cells, to create germ egg cells), and genetic engineering (sequencing the genomes from museum specimen DNA, and editing DNA in cells from living forms to produce a match).

Literature Review: Mammal Evolution

by Carl Strang

Today’s collection of notes from the 2013 scientific literature focuses on mammals and their evolution. As the notes reveal, some of these topics are controversial among researchers.

This migrating bat chose a famous resting place during its journey: the Aldo Leopold shack in Wisconsin. Bats are the subject of two of the following studies.

This migrating bat chose a famous resting place during its journey: the Aldo Leopold shack in Wisconsin. Bats are the subject of two of the following studies.

Chang-Fu Zhou, Shaoyuan Wu, Thomas Martin, Zhe-Xi Luo. 2013. A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations. Nature 500 (7461): 163 DOI: 10.1038/nature12429  They described a newly discovered Jurassic proto-mammal, Megaconus mammaliaformis, and found evidence that traits such as hair and fur originated well before the rise of the first true mammals. The squirrel-sized Megaconus had a heel spur, similar to poisonous spurs found on modern egg-laying mammals, such as male platypuses. It had mammalian dental features, and legs and feet that point to a gait similar to that of modern armadillos. At the same time it had a reptilian middle ear, ankle bones and vertebral column.

O’Leary, Maureen, et al. 2013. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339:662-667. Using fossil materials and an extensive character analysis, they conclude that the ancestral placental mammal from which all major surviving groups evolved lived just after the beginning of the Paleocene. This conflicts with molecular clock data that place the appearance of many groups including bats, rodents, and even-toed ungulates back in the Cretaceous. They combine the characters of the early fossils to produce a hypothetical common ancestor, an insectivorous animal resembling a shrew with a long tail.

Zhang, Guojie, et al. 2013. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science 339: 456-460. They did whole-genome comparisons of nuclear DNA of a Myotis and a flying fox. Significant sequences were found which may relate to the development of flight ability, and the immune systems also are different from those of other mammals. When compared to the genomes of other mammals, bats fall out most closely related to perissodactyls, then carnivores, with those groups splitting apart at an estimated time in the Cretaceous.

Ni, Xijun, et al. 2013. The oldest known primate skeleton and early haplorhine evolution. Nature 498 (7452): 60 DOI: 10.1038/nature12200  They describe a 55mya (early Eocene) Chinese fossil that is in the tarsier line but has features showing it to be close to the branch point leading to the tarsiers in one direction, anthropoids (primates including monkeys, apes and humans) on the other. It is tiny, the animal around 1 ounce in weight. Asia appears to be the likely center of early primate evolution.

Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, et al. 2013. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet, 9(3): e1003345; DOI: 10.1371/journal.pgen.1003345  This most recent examination of polar bear and brown bear genetics concluded that, on the whole, polar bears have been separate from brown bears for about half the time that brown bears have been separate from black bears. The connections previously noted between the two species in southeast Alaska, and possibly in Ireland, appear to be the result of small polar bear populations being isolated during ice ages, and being swamped then by an influx of male brown bears. The polar bear is a more ancient species than that.

Zigouris J, Schaefer JA, Fortin C, Kyle CJ. 2013. Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution. PLoS ONE 8(12): e83837. doi:10.1371/journal.pone.0083837  Their analysis of mitochondrial and nuclear genes points to a single population of wolverines surviving the glacial maximum in a refugium somewhere in the Old World, then expanding into North America across the Bering Sea land bridge as the glaciers retreated. Subsequently, several North American populations differentiated. The fossil record likewise has them only in Eurasia prior to the late Pleistocene.

Andrew M. Minnis, Daniel L. Lindner. 2013. Phylogenetic evaluation of Geomyces and allies reveals no close relatives of Pseudogymnoascus destructans, comb. nov., in bat hibernacula of eastern North America. Fungal Biology, DOI: 10.1016/j.funbio.2013.07.001  As described in a ScienceDaily article. The closest relatives of the fungus causing white nose syndrome are species that live in European caves. This supports the idea that the fungus is an invasive species here, but one with which European bats coevolved and so have some immunity.

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