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.

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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: 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.

Editorial: Creationism = Idolatry?

by Carl Strang

This is an extension of the Winter Campfire series of several years ago.

This is an extension of the Winter Campfire series of several years ago.

I debated whether or not to finish this post’s title with the question mark, but this is after all a blog about inquiry, so I went with that punctuation. This also is a blog about science, but as I have ventured into the relationship between science and spirituality in the Winter Campfire series, it seems appropriate to comment on creationism.

This is not a general comment on all manifestations of creationism, however. Hopi creationism, for example, comes out of a tradition apart from Western science. Here I am focused on creationism as expressed by certain conservative Christian sects.

The problem I have with this creationism is an inherent ironic tension within it. The defining claim is that the Universe is a created thing, and though creationists sometimes are coy in their language, it is clear enough that their creator is a traditional, bearded-male-in-the-sky, supernatural God who stands separate from this creation. So, let’s take all that as a given and see where it leads us. If the Universe indeed was created by such an entity, it also must be regarded as a text written by that entity. Many early natural scientists in fact took it as part of their mission to read this text through their scientific work so that science for them illuminated the workings of God. Science has become secularized, but that does not change the fact that if the Universe indeed was created, its scientific study is a reading of it as a text, and a religious person could say that it is a direct reading of the text as written by the Universe’s creator.

So, why does this represent such a problem to the creationists? We seem to have a disagreement between texts. On the one hand we have a text written, as the creationists would say, by God, and read by the scientists. This God’s text clearly includes evolution as a major theme. On the other hand we have the Bible. One might argue that the Bible was divinely inspired, but if so then we have to acknowledge that it was filtered through imperfect, error-prone human minds. Furthermore, the Bible also is a political document, its contents the result of a biased debate and compromise on which of the many candidate books and texts to include, and which to leave out. In other words, its edited table of contents is the product of still more imperfect human influence.

So when the direct reading of a text written by God is rejected in favor of a text written by man, I cannot see how one can regard Christian creationism as anything other than idolatry, with a book taking the place of the golden calf of the Mosaic story.

This should not be taken as a devaluation of the Bible. That book is a significant body of history, legend, and metaphor, written by ancient Middle Easterners for whom poetry and layered meanings were primary. Read through that lens, the Bible can be an enriching guidebook. It is an error to think that it, any more than the traditional stories of any culture, can be regarded as a work of western scientific nonfiction.

 

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.

Literature Review: The Paleozoic Era

by Carl Strang

Last week I shared notes on some published papers from last year which cast light on the early Earth, when life first appeared. The Paleozoic Era was marked by the sudden appearance of abundant, diverse new fossils. What has become increasingly clear is that readily fossilized shells were the major new development, making the “Cambrian explosion” possible (the Cambrian Period is the opening chapter of that era).

Smith, M. Paul, and David A.T. Harper. 2013. Causes of the Cambrian explosion. Science 341:1355-1356. They reviewed major themes that have emerged from research in this area. Some important components are the rising sea/sinking continents which released high mineral concentrations into the oceans (providing material for constructing shells), along with the huge increase in shallow sea habitat (providing much area in which ecological interactions could take place, including predator-prey interactions which would drive the evolution of shells for prey protection and improved predator effectiveness), and growing evidence that earlier, Proterozoic organisms in fact were ancestors of Cambrian groups, which includes molecular clock estimates as well as fossil connections.

Diverse marine invertebrates appeared in the early Paleozoic.

Diverse marine invertebrates appeared in the early Paleozoic.

Jie Yang, Javier Ortega-Hernández, Nicholas J. Butterfield, Xi-guang Zhang. Specialized appendages in fuxianhuiids and the head organization of early euarthropods. Nature, 2013; 494 (7438): 468 DOI: 10.1038/nature11874  From a ScienceDaily article. They described fossils of an early-Cambrian-explosion arthropod, Chenjiangocaris kunmingensis, in which the anterior-most limbs are modified for feeding, apparently for shoveling sediment into the mouth. It was generally soft-bodied, but had a carapace. This is also the earliest known species with a central nervous system extending back from the head. It came from a new site in south China called Xiaoshiba which promises to provide many additional insights into the earliest evolution of animals.

The appearance of shells in the Cambrian, probably resulting from predator-prey interactions, made abundant fossils from that time a possibility.

The appearance of shells in the Cambrian, probably resulting from predator-prey interactions, made abundant fossils from that time a possibility.

Tanaka,Gengo, et al. 2013. Chelicerate neural ground pattern in a Cambrian great appendage arthropod. Nature 502 (7471): 364 DOI: 10.1038/nature12520  From a ScienceDaily article. They described a new species whose central nervous system is preserved well enough to show that it was a chelicerate arthropod, and thus that chelicerates split from mandibulates more than 520 million years ago. Alalcomenaeus belonged to an extinct group of large-clawed arthropods, the megacheirans, that previously had been difficult to place. It had two pairs of large eyes at the front of the head. Earlier, a similar analysis of another Chinese fossil from this deposit, Fuxianhuia, revealed a nervous system that connected it to the crustaceans, which are mandibulates (chelicerate and mandibulate arthropods are the two major groups, the former today including spiders and scorpions, the latter insects and crabs, among others).

Jean-Bernard Caron, Simon Conway Morris, Christopher B. Cameron. Tubicolous enteropneusts from the Cambrian period. Nature, 2013; DOI: 10.1038/nature12017  As reported in ScienceDaily. They described an acorn worm or hemichordate, Spartobranchus tenuis from the Burgess Shale, which is the oldest of its group by 200 million years. Its group is one of the two main groups of hemichordates, and this fossil ties the two together, as well as having connections to echinoderms and chordates. They were extremely abundant in places, and may have been important marine sediment dwellers, their function similar to terrestrial earthworms today.

Pennisi, Elizabeth. 2013. Eating was tough for early tetrapods. Science 339:390. This news article covered recent research on early terrestrial vertebrates (from much later in the Paleozoic than the species mentioned above) that looked at the challenge posed by swallowing prey on land rather than in the water. Developing that capability may have taken 80 million years, with early ones feeding in the water or carrying captured prey into the water where they could have swallowed it along with gulps of water. At some point, tongues evolved that could assist.

Linda A. Tsuji, Christian A. Sidor, J.- Sébastien Steyer, Roger M. H. Smith, Neil J. Tabor, Oumarou Ide. The vertebrate fauna of the Upper Permian of Niger—VII. Cranial anatomy and relationships of Bunostegos akokanensis (Pareiasauria). Journal of Vertebrate Paleontology, 2013; 33 (4): 747 DOI: 10.1080/02724634.2013.739537  As described in a ScienceDaily article. This pareiasaur was endemic to the center of Pangaea, which has been established geologically as a desert region (the continents fused together in the late Paleozoic, and the resulting supercontinent of Pangaea had an interior far from any sea). Apparently that region was so distinct from surrounding more moderate biomes that the boundary served as an isolating barricade for species on either side. This one was a cow-sized herbivore.

Literature Review: Wolves and Dogs

by Carl Strang

Last year produced a few published studies of wolves and dogs that caught my eye. Dogs are well established as having been domesticated from wild wolves, but the timing and nature of that new relationship have been a contentious topic. Here is a recent contribution to the debate:

Thalmann, O., et al. 2013. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342:871-874. This group of researchers previously had suggested that dogs first were domesticated in the Middle East, but this new study with updated methods points to a European origin 18-32,000 years ago. They included DNA from fossil wolves and dogs in their comparisons. From an interpretive article in ScienceDaily: “By comparing this ancient mitochondrial DNA with the modern mitochondrial genomes of 77 domestic dogs, 49 wolves and four coyotes, the researchers determined that the domestic dogs [of today] were genetically grouped with ancient wolves or dogs from Europe — not with wolves found anywhere else in the world or even with modern European wolves. Dogs, they concluded, derived from ancient wolves that inhabited Europe and are now extinct.” This timing and geography point to a likely domestication by hunter-gatherers rather than agriculturalists.

Wolf at Wolf Park in Indiana

Wolf at Wolf Park in Indiana

Once the ancestors of dogs had become genetically isolated from wolves, the two populations were exposed to different selective pressures. The wolves continued to be subject to natural selection, while the dogs were influenced by human-directed selective breeding, and by the different selective pressures of living in human communities. The next study compared the development of dogs and wolves, and discovered some consequences of that divergence.

Kathryn Lord. A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris). Ethology, 2013; 119 (2): 110 DOI: 10.1111/eth.12044 From a ScienceDaily article. She looked at the relationship between the timing of sensory maturation and exploration behavior in wolf and dog puppies. Both acquire smell, hearing and vision in that order, at 2, 4 and 6 weeks of age. Wolves, however, begin exploration and socialization at 2 weeks, dogs at 4 weeks, and so dogs are socializing after they have the ability to perceive their social surroundings more completely. Wolves are getting fearful shocks during this period as new sensory capabilities appear, and so need an earlier and more complete contact with their social community, and never form the same kind of solid bond that dogs do.

Dogs have diverged from their wolf ancestors

Dogs have diverged from their wolf ancestors

A final, sadder note was a news article in Science magazine that explained how Isle Royale’s long-studied wolves are close to dying out.

Wolf tracks on an Isle Royale beach. Are these about to disappear?

Wolf tracks on an Isle Royale beach. Are these about to disappear?

Mlot, Christine. 2013. Are Isle Royale’s wolves chasing extinction? Science 340:919-921. Last year, for the first time in 40 years, there were no wolf pups on the island. The 2013 January count turned up only 8 closely related adults. Rolf Peterson, principal wolf biologist at Isle Royale for many years, thinks they now will die out, with inbreeding the root cause. Moose have increased as their principal predators have declined. The Park Service is considering whether to introduce new wolves to rescue the population (Isle Royale is a national park in northern Lake Superior).

Literature Review: Lagomorph Evolution

by Carl Strang

This week’s literature review focuses on a study of the evolutionary history of the mammalian order Lagomorpha, the rabbits, hares and pikas (the members of this group, by the way, are separate from Rodentia, the rodent order, though the two are closely enough related that there is a term, glires, for the two orders combined). This study was reported in the open on-line journal PLoS ONE.

Ge D, Wen Z, Xia L, Zhang Z, Erbajeva M, et al. (2013) Evolutionary History of Lagomorphs in Response to Global Environmental Change. PLoS ONE 8(4): e59668. doi:10.1371/journal.pone.0059668

Pikas today are represented by relatively few high-altitude dwellers.

Pika, Rocky Mountains National Park

Pika, Rocky Mountains National Park

In the first half of the Miocene epoch, roughly 25-30 million years ago, pikas were much more widespread and diverse, and were represented by more than 20 genera. This was, however, a time of climatic warming and drying, a major result of which was the spread of grasslands and the evolution of plants physiologically adapted to the new climate. Most pika varieties went extinct, the survivors becoming isolated in higher altitudes or latitudes where they could continue to find plenty of plants with the older physiology that they could eat.

Pika collecting food

Pika collecting food

The change benefited the other branch of Lagomorpha, the rabbits and hares, which diversified and expanded their collective range.

Eastern cottontail

Eastern cottontail

Though their diversity has decreased after peaking around 5 million years ago during the transition from the Miocene to the cooler Pliocene, rabbits and hares today remain much more widespread and diverse than the pikas.

Literature Review: Turtle Evolution

by Carl Strang

I have long had a fondness for turtles. These strange animals were diverse and abundant in the lake below my childhood home. Two studies of this group caught my eye in 2013.

Wang, Zhuo, et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics, 2013; DOI: 10.1038/ng.2615

As described in a ScienceDaily article. This was a genomic study with an evo-devo component that looked at those two highly different turtle species. They placed the turtles with the archosaurs (the group including dinosaurs, birds and crocodiles) rather than being more primitively reptilian. They place the split of the turtle line at 250 million years ago, coinciding with the great end-Permian extinction. Shell development makes use of genes connected with limb development (perhaps bone-extending elements that expand the ribs and sternum to form the shell? This article did not get that specific). Turtles also are found to have the greatest range of odor detection capability in vertebrates other than mammals.

A sea turtle, either the green sea turtle of the previous study or a close relative.

A sea turtle, either the green sea turtle of the previous study or a close relative.

Tyler R. Lyson, Gabe S. Bever, Torsten M. Scheyer, Allison Y. Hsiang, Jacques A. Gauthier. Evolutionary Origin of the Turtle Shell. Current Biology, 2013; DOI: 10.1016/j.cub.2013.05.003

From a ScienceDaily article. They described a fossil from South Africa, Euntosaurus africanus, which is a transitional turtle. The ribs are widened but not fused. This animal lived 260 million years ago, in the Permian. Turtles had complete shells by 215 million years ago. Odontochelys semitestacea, a previously described Chinese fossil of 220 million years ago, had a complete plastron but incomplete carapace.

The first study used genetic methods, and therefore molecular clock estimation, to place the timing of turtle evolution. The agreement with the fossil aging in the second study is impressive.

Literature Review: Fungal Evolution

by Carl Strang

Fungi work behind the scenes for the most part, but they have played, and continue to play, essential roles in Earth’s ecosystems. That important work began a long time ago.

We most often notice fungi at the brief times when they grow spore-dispersing structures.

We most often notice fungi at the brief times when they grow spore-dispersing structures.

Floudas, Dimitrios, et al. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336:1715-1719.

Comparative genomic and molecular clock analyses in fungi “suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous Period.” In other words, the immense volumes of Paleozoic coal accumulated because fungi had not yet evolved the ability to decompose wood down into its nutritious chemical components. After they did so, much less wood survived to become coal.

Wolfe BE, Tulloss RE, Pringle A (2012) The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis. PLoS ONE 7(7): e39597. doi:10.1371/journal.pone.0039597

They looked at the genetics of nutrition in Amanita fungi, and found that their mutualistic partnerships with vascular plants are obligate. The fungi have lost two genes that once allowed them to decompose organic matter in the soil, so that they now depend upon their mutualistic partners for carbon. This study refers to another very important ecological role many fungi play. They form partnerships with many green plants, channeling in soil minerals in exchange for other goodies. As the authors point out, this trade no longer is an option: the partners can’t survive without it.

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