Literature Review: Periodical Cicadas

by Carl Strang

This week’s literature focus is on a single paper, which looked at a significant aspect of periodical cicada biology.

The northern periodical cicada species, Linnaeus’s 17-year cicada on the left, Cassin’s 17-year cicada on the right

The northern periodical cicada species, Linnaeus’s 17-year cicada on the left, Cassin’s 17-year cicada on the right

Karban, Richard. 2014. Transient habitats limit development time for periodical cicadas. Ecology 95:3-8. He studied septendecim and cassini (our two local species of Magicicada) in New York state. There are several hypotheses explaining why their development times are so long: Pleistocene historical influences (long life span buffered annual climate variation in glacial refuges), predator satiation (some early maturing individuals wait for slower ones to catch up, and long life spans facilitate this), low nutrition forces long development, and increased fecundity (17-year species have been shown to be more fecund than the more southern 13-year versions). Here he examined the possibility that habitat quality changes rapidly enough to put an upper limit on such advantages of long lifespans. Though past studies pointed to possible advantages of edge trees, here he compared weights of newly eclosed adults from edge vs. forest interiors, finding the former to be only slightly (4.9%) heavier in septendecim but no difference in cassini. He took density of emerging nymphs as an indication of habitat quality. Changes in study sites were significant between emergences, enough to limit any advantage of longer life. He commented on the Raccoon Grove study site in Will County, once one of the highest-density populations known, mentioning that they plummeted over just a couple sequential emergences, first because of Dutch elm disease killing host trees. Karban and Yang visited that site in 2007, hearing one chorus but finding no emergence holes or nymphal skins.

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: 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: Whole Genome Comparisons

by Carl Strang

Another hot area of biological research these days is the comparative study of whole genomes, the entire DNA sequences of different species. Birds received a lot of this sort of attention in 2014 publications, but the following notes also include interesting studies of insects and crocodilians.

Zhang, Guojie, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320. They compared whole genomes of 48 species across the range of living species. Of the 37 orders, 34 are represented, the missing ones being some of the ratite groups (only tinamous and ostrich included). The genome is smaller than those of other amniotes, through loss of repetitive sections and large deletions. There are large areas shared by all birds, but plenty of areas where genes vary according to lifestyles, as well as convergences. They looked at vocal learning, which occurs in songbirds, parrots and hummingbirds, and earlier had been shown to have common brain circuits for song learning not present in other birds. Genomes showed convergence in the underlying protein-coding and regulatory genes, absent in birds that don’t learn songs. They also identified genes associated with bird skeletal development, lung structure, and feathers. Teeth were absent in the common ancestor of all modern birds, rather than being lost more than once. Birds have more genes for color vision than mammals, and the ancestral bird is supported as tetrachromatic.

Among the many interesting points from the following study is that falcons like this kestrel are more closely related to parrots than they are to hawks and eagles.

Among the many interesting points from the following study is that falcons like this kestrel are more closely related to parrots than they are to hawks and eagles.

Jarvis, Erich D., et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331. Whole genomes proved problematic in phylogenetic analysis, thanks to convergences in protein coding portions and the jumble of rapid diversification in the early Paleogene. Non-coding sections, however, provided a more consistent picture. Some highlights: Anseriformes (ducks, geese, etc.) plus Galliformes (chickens etc.) are closest (sister) to one another, their combined Galloanseres group separate from “Neoaves” (together with them forming “Neognathae,” separate from Palaeognathae or ratites). Flamingoes and grebes are sister groups, confirming the earlier Field Museum study, with the next-closest local birds the pigeons and doves, all combined into “Columbea” vs. “Passerea” as the divisions of Neoaves. Hummingbirds are sister to swifts, then nightjars. Cranes are sister to shorebirds. Loons are sister to a cluster of water bird orders including pelicans, herons, tube-nosed seabirds, and penguins. New World vultures are sister to eagles and other Accipitriformes. Owls are sister to a cluster of orders with only woodpeckers represented locally. Oscines are sister to suboscines, together to parrots, then falcons. Groups charted as existing by the end of the Mesozoic are Palaeognathae, Galloanseres, Columbea, and Passerea, with nearly all orders in existence by 50 million years ago. The splits more recent than that are those between hummingbirds and swifts (both contained within order Caprimulgiformes), Coraciiformes (including kingfishers) and Piciformes (including woodpeckers), and oscines and suboscines within Passeriformes.

Romanov, Michael N., et al. 2014. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15 (1): 1060 DOI: 10.1186/1471-2164-15-1060  Their portion of the avian whole-genome comparison project found that chickens and turkeys most resemble the computed common ancestor of birds and other dinosaurs.

Mitchell, Kieren J., et al. 2014. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science 344:898-900. They sequenced elephant bird DNA (extinct species from Madagascar) and found, surprisingly, that this was the New Zealand kiwi’s nearest relative. Their study concluded that the ratites (emu, ostrich, rhea, kiwi, etc.) descended from flying ancestors that once were widespread and dispersed easily. After the dinosaurs were gone, the larger ratites were able to fill some large-herbivore niche space and the various groups independently evolved into large flightless forms. That evolutionary window closed as the mammals caught up, except for isolated islands where, for instance, the dodo evolved. Continental drift separated some large flightless ratites geographically, but ancestral flight also contributed as indicated by the New Zealand-Madagascar connection.

Insect flight was fostered by the first forests, which created the 3-dimensional framework that made flight advantageous.

Insect flight was fostered by the first forests, which created the 3-dimensional framework that made flight advantageous.

Misof, B., et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763-767. They did a massive genomic comparison across the insect class, and highlights include indications that insects first appeared 479mya (million years ago, Early Ordovician), coincident with the first land plants. They first developed wings 406mya (Early Devonian; the oldest insect fossils date to 412mya), becoming the first flying animals, at about the same time plants grew larger and began to produce forests, creating a 3D environment in which flight would be especially advantageous. Major lineages of today trace back to the Mississippian (345mya), and the major diversification of insects with complete metamorphic development happened in the Early Cretaceous.

American alligators are genetically very close to the other crocodilians.

American alligators are genetically very close to the other crocodilians.

Green, R.E., et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346 (6215): 1254449 DOI: 10.1126/science.1254449  Whole-genome comparisons found that crocodilians are very similar to one another (93% similarity among species), and have changed very slowly. This slow evolutionary pace, shared with the nearest outgroup of crocodilians + birds, the turtles, indicates that the shared ancestor likewise evolved slowly, and that some time after the split, avian ancestors evolved the capacity for rapid evolution that set the stage for rapid diversification after the other dinosaurs went extinct.

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.

Literature Review: Squirrel Communication

by Carl Strang

Those who dislike tree squirrels regard them as rats with bushy tails. Those bushy tails are important in many ways, however. They provide insulation when wrapped around the animal in its nest, and they also are used in communication. Two studies in 2014 focused on tail communication and, in one case, vocalizations. Both studies are ongoing but incomplete, as my notes indicate, but I include them here to remind us that these common animals have something to teach us if we pay attention.

Fox squirrel

Fox squirrel

University of Miami. 2014. “Predicting the predator threatening a squirrel by analyzing its sounds and tail movements.” ScienceDaily, <www.sciencedaily.com/releases/2014/10/141021125943.htm>. This article describes Ph.D. thesis work by Thaddeus McRae on the vocal and visual signals given by tree squirrels in the presence of various predators. “He measured the response of three distinct squirrel sounds: the “kuk” (a short bark), the “quaa” (a longer squeal) and the “moan” (a whistling sound). He also looked for specific patterns for tail motions in combination with these noises. The “twitch” involves a controlled movement in an arc shape, while the “flag” can take the shape of an arc, figure eight, circle or squiggle.” The article does not say which signals are associated with which predators, so future publications by this author will need to be found.

Pardo, Michael A., Scott A. Pardo, and William M. Shields. 2014. Eastern gray squirrels (Sciurus carolinensis) communicate with the positions of their tails in an agonistic conflict. Am. Midl. Nat. 172:359-365. They filmed squirrels’ aggressive interactions at feeders, determining dominance (who chases who) and tail position (tightness of bend, 5 levels varying from straight up to sharply bent; and portion bent, 3 levels varying from straight to tip-only bent, to bent about in the middle). Degree of aggression ranged from none to continuing a chase after a subordinate flees. Degree of aggressiveness by the dominant was influenced by the subordinate’s tail position as well as by the dominant’s. For instance, a dominant with a tightly bent tail showed the lowest aggression when the subordinate bent a large portion of its tail. When the dominant bent a small portion of its tail and the subordinate’s tail was loosely bent, the dominant showed low aggression, but this shifted to the highest level when it bent a large portion of its tail and the subordinate’s was tightly bent.

Literature Review: Bird Species Boundaries

by Carl Strang

I’ll begin my review of the 2014 scientific literature with my notes on three interesting studies of birds. These focus on two kinds of boundaries between species: range boundaries that sometimes result in hybrid zones where the adjacent species are closely related; and the biological species definition, in which species are separated by their inability to hybridize freely. When hybrids reproduce less effectively than the parent species, the parent species are legitimate.

Black-capped Chickadee

Black-capped Chickadee

Taylor, Scott A., et al. 2014. Climate-mediated movement of an avian hybrid zone. Current Biology, DOI: 10.1016/j.cub.2014.01.069

They studied the northward advance of Carolina chickadees, the southern boundary of the black-capped chickadee range, and the hybrid zone between them. The average northward advance is 0.7 mile per year. The mapped boundary extends across northern Indiana in the third or fourth tier of counties, but westward plunges south so that in Illinois, it angles down roughly from Kankakee County to St. Louis. The hybrid zone in Pennsylvania, where the most intensive part of the study was done, averages 21 miles wide. The narrowness and evanescence of that zone results from hybrids being less successful than either parent species. Female Carolina chickadees are dispersing northward faster than males, and disperse about 0.6 mile per year, so they are the focus of the expansion. The average winter low temperature has advanced at the same speed as the chickadee shift, so by that measure climate likewise is moving north 0.7 mile per year.

Tobias, Joseph A., et al. 2013. Species coexistence and the dynamics of phenotypic evolution in adaptive radiation. Nature, DOI: 10.1038/nature12874

From a ScienceDaily article. They looked at evolutionary relationships in the large family of tropical ovenbirds (over 300 species, unrelated to the North American warbler of that name). They were interested in testing the degree to which competition among closely related species pushes their evolutionary divergence. Estimated ages of divergence revealed that competition did not play a role in speciation, as the species had diverged millions of years before they were brought together in the same places. Though instances are known in which young species diverge through competition, the overall pattern found in these coexisting species did not involve that process. One result that seems contrary to the expected pattern is that coexisting species evolved convergent, rather than divergent, songs. This may allow them to space their territories not only with respect to members of their own species, but also with respect to members of closely related species, which would be their closest competitors. Though the authors seem to want to generalize this to evolution of animals broadly, this seems unjustified at least for now.

Poelstra, J.W., et al. 2014. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344:1410-1414.

De Knijff, Peter. 2014. How carrion and hooded crows defeat Linnaeus’s curse. Science 344:1345-1346.

The de Knijff article interprets the Poelstra paper. This study looked at carrion crows and hooded crows, which have a hybrid zone in central Europe and northern Britain between their otherwise separate ranges. Some have argued that they should be regarded as subspecies because of the hybridization, but this study found that a tiny portion of the genome (less than 1%, tied to an inversion of part of a chromosome), related to feather pigmentation and visual perception, is a solid separator of the species genetically. Cases like this challenge bar code species demarcation, which requires at least a 10% genomic difference. The species separation, the authors state, is based not on separate ecology but rather on sexual selection alone.

Literature Review: Arthropod Evolution

by Carl Strang

If you’re a bug nerd you’ll enjoy the following notes on research from 2013. Especially significant were studies of butterflies and moths, and an eye-opening paper on periodical cicadas. This concludes my literature review until next winter.

Butterflies and moths had their origin in the Triassic Period according to recent studies, though the first ones were more like caddis flies than like this red-spotted purple.

Butterflies and moths had their origin in the Triassic Period according to recent studies, though the first ones were more like caddis flies than like this red-spotted purple.

Zhang, W, et al. 2013. New fossil Lepidoptera (Insecta: Amphiesmenoptera) from the Middle Jurassic Jiulongshan Formation of northeastern China. PLoS ONE 8(11): e79500. doi:10.1371/journal.pone.0079500  They found 15 species of early moths representing at least 3 families in Chinese deposits, and details of wing venation led to the conclusion that the Lepidoptera (moths and butterflies) diverged from the Trichoptera (caddis flies) by the early Jurassic Period.

Wahlberg, N, CW Wheat, C Peña 2013. Timing and patterns in the taxonomic diversification of Lepidoptera (butterflies and moths). PLoS ONE 8(11): e80875. doi:10.1371/journal.pone.0080875  They estimated timings of major episodes of speciation in the major groups of butterflies and moths. Their results point to a Triassic origin of Lepidoptera, around 215 million years ago. The timing of diversification episodes at least in some cases corresponds to times when plants were diversifying, and also after the end-Cretaceous mass extinction. Coevolution of lepidoptera with their larval food plants appears to be an important theme. They give origin ages for major Lepidoptera groups (in millions of years ago): Gracillarioidea 120, Yponomeutoidea 117, Glechioidea 106 (these first three are small moths, many of them leaf miners), Papilionoidea 104 (butterflies), Pyraloidea (including many local pyralid moths) 93, Bombycoidea (including sphinx moths) 84, Geometroidea (including inchworm moths) 83, Noctuoidea (the enormous owlet moth group) 82, Tortricoidea (including leaf-folding caterpillars) 68. All these groups are represented by local species.

The Chicago region’s 17-year periodical cicadas: Magicicada septendecim, left, and M. cassini.

The Chicago region’s 17-year periodical cicadas: Magicicada septendecim, left, and M. cassini.

Sota, Teiji, Satoshi Yamamoto, John R. Cooley, Kathy B.R. Hill, Chris Simon, and Jin Yoshimura. 2013. Independent divergence of 13- and 17-y life cycles among three periodical cicada lineages. Proc. Nat. Acad. Sci. 110:6919-6924. They sequenced a number of genes from nuclear and mitochondrial DNA from all known species and broods, and estimated divergence times based on general research that has been done on insect mitochondria. There are three species groups (referred to as Decim, Cassini, and Decula), each of which contains northern 17-year species and southern 13-year species. In any location, the species in the different groups emerge at the same time. The results clearly separated the three groups, and tied together the species within each group (e.g., 13-year Decim are more closely related to 17-year Decim than to 13-year Cassini). Furthermore, each species group is divided into eastern, central and western genetic clusters (this pattern has been documented in other organisms as well; for the most part, Illinois cicadas are in western clusters, Indiana ones in central clusters). Each cluster contains both 13- and 17-year species, “suggesting that life cycle divergence occurred independently in the three regions.” Analyses estimated that the western Cassini divergence of 13-year and 17-year species took place 23,000 years ago, 10,000 years for Decim. Population sizes for both Decim and Cassini groups appear to have been small during the last glacial period, but expanded greatly starting 10,000 years ago. The sequence appears to have been allopatric speciation of the 3 ancestral species, with the species later becoming sympatric and independently splitting into 13- and 17-year cicadas. “Surprisingly, however, the divergence of 13- and 17-y cicadas was asynchronous among the species groups and occurred repeatedly even within a species group.” The implication is “that the three Magicicada groups shared multiple refugia during the last glacial maximum.” The 13-/17-year splits occurred after the last glacial maximum, within the last 23,000 years, “suggesting that the life cycle divergence in Magicicada is closely associated with global climatic fluctuations and shorter growing seasons in the north versus the south.” However, the species groups themselves separated in the Pliocene, and their shared long lives suggest that this did not originate because of glacial climate influences. This shifting between 13- and 17-year life cycles suggests a common genetic basis among the species, and indicates a somewhat plastic nature of this trait. The coordination among species at a given location seems best explained by the selective advantage of low numbers of an invading species into the range of another, surviving best when sheltered by the established species’ numbers.

Zhao, Z, et al. 2013. The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of tachinid flies. PLoS ONE 8(4): e61814. doi:10.1371/journal.pone.0061814  Their genomic study traced the evolutionary relationships of the parasitic fly family Tachinidae, and molecular clock analysis calibrated to the fossil record points to the middle Eocene as the time of the family’s origin.

Brewer, MS, and JE Bond. 2013. Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses. PLoS ONE 8(11): e79935. doi:10.1371/journal.pone.0079935  They place the ancestral millipedes at 510mya (million years ago), with major groupings established by 200mya.

Lucky, A, MD Trautwein, BS Guénard, MD Weiser, RR Dunn. 2013. Tracing the rise of ants – out of the ground. PLoS ONE 8(12): e84012. doi:10.1371/journal.pone.0084012     A phylogenetic analysis points to soil rather than leaf litter as the nesting habitat for the earliest ant species.

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