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: 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.

A Stream Community

by Carl Strang

(This is a cross posting from the Observe Your Preserve website). Mussels and fishes are the larger aquatic animals living in our local streams. The rescue operation at West Branch Forest Preserve, described yesterday, provided information on the diverse species in that site. Though empty mussel shells indicated an even more diverse past, still, four common species remain.

Left, white heelsplitter; top, giant floater; bottom, fatmucket; right, plain pocketbook

Left, white heelsplitter; top, giant floater; bottom, fatmucket; right, plain pocketbook

All are filter feeders, opening the question of how they manage to coexist. If they all subsist on the same food, we might expect the best competitor to push the others out of the picture, unless a superabundance of the food prevents it from being a limiting factor. As it happens, though, there are at least two ways in which mussels separate themselves ecologically. One is by having different larval hosts. Mussels begin life as larval forms attached to the gills of fishes. Different kinds of mussels are hosted by different fish species. In fact, one reason for the loss of some mussel species from that portion of the West Branch is that their host fishes no longer live there. Another ecological separation of mussels is through substrate preference. Some mussels like silt (the giant floater is an example), some prefer sand (the white heelsplitter in this community), others heavier gravel (plain pocketbook, fatmucket). Some like stronger current, others the slower pools.

Fishes likewise prefer different portions of the stream. Pools are home for bullheads, though black bullheads are more tolerant of silt than are yellow bullheads.

Black bullhead

Black bullhead

Yellow bullhead

Yellow bullhead

Swifter current is associated with more of a gravel bottom, preferred by creek chubs and sand shiners.

Creek chub

Creek chub

Sand shiner

Sand shiner

Largemouth bass, black crappies and green sunfish hunt other animals in more open waters, while white suckers are adapted to bottom feeding.

Largemouth bass

Largemouth bass

Black crappie

Black crappie

Green sunfish

Green sunfish

White sucker

White sucker

Pumpkinseeds prefer pools with plenty of vegetation, and prefer snails as food. They, and quillbacks, are less common than generalists like the green sunfish.

Pumpkinseed

Pumpkinseed

Quillback

Quillback

Together, they sort out the different habitats within the river and form the fish community revealed during the rescue operation. For more information on these and other species, go to the individual species pages in the Observe Your Preserve website.

West Branch Rescue Mission

by Carl Strang

(Note: This is a cross posting from the Observe Your Preserve website, a reference for all the forest preserves in DuPage County, their ecosystems and organisms, natural and cultural history).

The Forest Preserve District currently is engaged in a 350-acre wetland and prairie restoration project at West Branch Forest Preserve. Section by section, a mile-long stretch of the West Branch of the DuPage River is being diverted into a temporary channel while the main reach of the stream is improved: the unhealthy vertical banks receive a gentler profile, root logs are jammed into the outside bends to stabilize them, and riffles and pools are created to diversify the habitat and maximize the number of species that can live there.

A temporary dam sends the river into its temporary channel.

A temporary dam sends the river into its temporary channel.

The temporary channel is lined with plastic to prevent erosion.

The temporary channel is lined with plastic to prevent erosion.

The completed restoration of the channel above the dam.

The completed restoration of the channel above the dam.

October 4 was devoted to a search and rescue mission. The first reach of the stream was complete, and a dam blocked the next section, the bypass ushering the water over a plastic lining that prevented erosion and soil loss. With the water drained from the corresponding part of river channel, fishes and mussels had become stranded in shallow pools, and these needed rescuing before that part of the river improvement could proceed.

Forest Preserve District natural resources staff, along with volunteers and county staff, waded in and transferred the mussels, bucketsful of them. Four native species, identified with such colorful names as white heelsplitter, fatmucket, plain pocketbook and giant floater, got a ride into their new digs upstream.

Sorting mussels

Sorting mussels

A richer past was revealed by the empty shells of additional species whose larval hosts had gone locally extinct (newly hatched mussels attach to the gills of fishes and live a temporary parasitic life). Stream improvement projects like this offer hope of a return to this past diversity. As for the fishes, a backpack electric shocker facilitated the netting of more than 10 kinds of them. The bass and crappies, shiners and chubs, bullheads, suckers, and sunfish temporarily resided in buckets with oxygen bubblers before being carried back to the main flowage.

The backpack shocker is flanked by netters.

The backpack shocker is flanked by netters.

Shocked fish float to the surface and are caught.

Shocked fish float to the surface and are caught.

Some of the rescued fishes.

Some of the rescued fishes.

The stream channel improvement is scheduled to be completed this year, with a large acreage of associated new wetlands and prairies on either side due to be built in 2014.

Lessons from Travels: Reefs

by Carl Strang

One of the most breathtaking experiences is that of tropical coral reefs. Whether you explore them by snorkeling, as I have done a few times, or take the plunge and scuba dive, the beauty of reef communities is so far removed from our everyday experience that it safely can be described as “out of this world.”

The shapes and colors of the corals and other fixed life forms are sufficient to satisfy the aesthetic need. But then add the diverse, colorful fishes and other freely moving animals, and the experience is transporting.

Beaches near reefs may be filled with the rubble from eroded coral formations, as well as mollusk shells and other remains of ocean life.

The pieces are reminiscent of fossils.

This brings us back home. Our bedrock in northeast Illinois and northwest Indiana is Paleozoic in age. It formed when our part of the world was a shallow sea, and was in fact punctuated by reef communities. There were corals, though they were not the ancestors of today’s corals. For most of that time fishes were absent or few. I think, though, that snorkeling or diving in those reefs would have been just as transfixing as today’s experience. The trilobites and other animals were diverse and active, some swam, and they well may have been as colorful and patterned as the reef animals of today.

Winter is edging in, and so we enter the season when tropical reefs seem most remote in time and space. One brief respite can be found in the prehistoric life exhibit at Chicago’s Field Museum of Natural History. There is an enormous animated wall that shows what a Cambrian reef might have been like, with the fixed forms, the slowly moving ones, the fast swimmers, the episodes of predation, all with a very relaxing background sound. I cannot visit that museum without spending a few minutes enjoying that scene. Sometimes lessons don’t need distant travel.

Dry

by Carl Strang

Last week was the first session of this year’s Roger Raccoon Club. One of the highlights always is the creek hike, which takes place during the overnight campout. We camp at Waterfall Glen Forest Preserve, and in the afternoon head over to Sawmill Creek and walk up that shallow stream to the dam, where we spend a good couple of hours. This time, though, we discovered a clear consequence of this year’s drought.

The streambed was dry for nearly all its length.

I don’t remember seeing this before. I knew, though, that there would be pools here and there, and the kids were eager to find what animals might have been concentrated in them.

The pools thus became collecting points for children as well as critters.

Crayfish were a popular focus of catch-and-release efforts.

Max shows one of the bigger ones.

There were minnows, as well, and a water snake.

Paige, whose reputation as the group’s champion frog-catcher was established on the first two days of the program, caught a bullhead that had taken refuge beneath a rock.

Most kids repeat the program, and so they either have seen the stream in its more typical flow, or will do so next year. Most of their best lessons are learned through direct experience of nature rather than through any jabbering I may do.

Literature Review: Paleozoic

by Carl Strang

This week’s assembly of papers from 2011 is a smattering of studies I encountered pertaining to the Paleozoic Era. In the Paleozoic we see the elaboration of multicellular life, first in the sea and then on land as both plants and animals solved the challenges of terrestrial life.

Peter Van Roy, Derek E. G. Briggs. A giant Ordovician anomalocaridid. Nature, 2011; 473 (7348): 510 DOI: 10.1038/nature09920     Anomalocaris is the most impressive predatory animal of the early Paleozoic, but this invertebrate previously was known only from the Cambrian Period which opened the era. This newly described species was larger than the Cambrian ones, at 3 feet long, and extends the group 30 million years beyond the Cambrian into the Ordovician Period.

G. D. Cody, et al. Molecular signature of chitin-protein complex in Paleozoic arthropods. Geology, 2011; DOI: 10.1130/G31648.1     They found surviving remnants of chitin and protein in a scorpion exoskeleton from the northern Illinois Pennsylvanian Period (310 million years ago) and in a eurypterid from Ontario’s Silurian Period (417 million years ago). The previous oldest preserved organic material was protein from dinosaur fossils. Ten years ago none of this would have been thought possible.

The next paper is about fish jaws such as this example of the extinct group known as placoderms. Field Museum of Natural History exhibit, Chicago.

Philip S. L. Anderson, Matt Friedman, Martin D. Brazeau, Emily J. Rayfield. Initial radiation of jaws demonstrated stability despite faunal and environmental change. Nature, 2011; DOI: 10.1038/nature10207     They did a comparative functional morphology study of early fish jaws across tens of millions of years, looking also at changes in fish communities. They found that jawless fish diversity was unchanged over 30 million years of overlap, calling into question the assumption that jawed fishes outcompeted them. When they did decline, there is no sign that jawed fishes expanded into abandoned ecological space. The initial diversification of jaw structure stabilized well before 400 million years ago, and subsequently remained stable in the face of significant environmental change.

Gerienne, Philippe, et al. 2011. A simple type of wood in two Early Devonian plants. Science 333:837. They describe slender fossil stems from France (407 million years ago) and from Canada (397 million years ago) that become the earliest examples of woody plants. Prior to this discovery, only herbaceous plants were known from this time, and the previous earliest woody plants were from the Middle Devonian, 397-385 million years ago. The size of the stems and details of their cellular structure support the idea that wood first evolved for fluid transport within the plant rather than for support. The timing of this development coincides with a drop in atmospheric carbon dioxide, which would have driven improvements in transport within the plant. The fossils resemble Psilophyton, a precursor of ferns and other vascular plants.

Club moss

Banks, Jo Ann, et al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960-963. They sequenced the genome of a club moss, Selaginella moellendorffii, and compared the result to the genomes of angiosperm plants. Both lineages are vascular, but they diverged shortly after vascular plants appeared 410 million years ago. Club mosses are much less diverse than angiosperms, and much less important ecologically. This may be related to their lack of whole-genome duplications which happened several times in angiosperm history. Most of the genes that direct angiosperm development are present in Selaginella. Comparisons with other groups indicate that the number of genes nearly doubled, from 3800 to 6800, between aquatic green algae and early land plants represented by mosses. A smaller increase of more than 400 genes characterized the common ancestor of Selaginella and Angiosperms, then there was a further increase of 1000 genes in the Angiosperms. After that the whole-genome duplications began.

Literature Review: Whole-Genome Duplications

by Carl Strang

One of the more significant but less publicized aspects of evolution is the importance of polyploidy. This is the rare form of mutation in which an organism’s genome is doubled. In other words, where once there was one set of genes now there are two. The descending members of that species, and the species that subsequently evolve from them, carry that doubled set. My literature review notes from the past year include two studies of this, one from plants and one from animals.

Our present-day plants have several polyploidy events in their evolutionary history (water knotweed).

Jiao, Yuannian, et al. Ancestral polyploidy in seed plants and angiosperms. Nature, 2011; DOI: 10.1038/nature09916

Their study of ancient plant lineages points to two polyploidy events that took place earlier than previously known ones, at 320 and at 192-210 million years ago. The earliest previously established such event was at 125-150 million years ago. With one of the two sets of genes able to carry on with their usual functions, the spares could mutate with much less potential impact on the organism. This expanded potential for evolutionary creativity made possible the huge diversity of plants we see today.

Arnegard, Matthew E., Derrick J. Zwickl, Ying Lu, and Harold H. Zakon. 2010. Old gene duplication facilitates origin and diversification of an innovative communication system—twice. doi: 10.1073/pnas.1011803107

Polyploidy events apparently happened less often, or at least are less studied, in animals. These researchers looked at two large groups of electric fishes in Africa and South America. Electric fishes have evolved in large muddy rivers, where visibility is very limited and there is an advantage to sensing their surroundings by measuring disturbances in electric fields. This study used evo-devo methodology, examining the genetic control of embryological development in an evolutionary context. They found that an ancient episode of duplication released a copy of a “voltage-gated sodium channel gene” for modification into a potential use in electric communication. In other words, the fishes went beyond simply sensing their surroundings and evolved the capability of using their electric field generators and sensors to communicate with one another. The two groups of fishes on the now separate continents shared the polyploidy duplication, and so had the same starting point. A subsequent sequence of events provided similar early modifications in the two groups, but then they followed different mutational pathways to reach essentially the same endpoint independently from one another. Today the fishes on the two continents have similar physiology and similar associated physical structures in their bodies, but that similarity is the result of convergence. The researchers estimate that the common endpoint was not reached until 100 million years after the genome duplication.

Fish Kill

by Carl Strang

On Tuesday of last week I returned to Mayslake Forest Preserve after the Labor Day holiday to find hundreds of small, dead bluegills floating in the east end of May’s Lake.

A sample of the fish kill.

They had been dead for a day or two, and they or possibly other afflicted fish had attracted a flock of gulls, a few cormorants and several herons of three species to the lake. I left a message with Forest Preserve District fisheries biologist Don LaBrose, and he got back to me later with the news that the immediate cause of death was columnaris disease, a bacterial illness in which Flexibacter columnaris produces lesions in the gills, and other damage.

Sometimes the lesions are obvious externally, sometimes you have to examine the gills.

Don’s reconstruction of events is that the shallow lake had a greatly reduced dissolved oxygen level, in part a consequence of this year’s hot summer. Lake water had reached a temperature of 80°F. This had stressed the fishes for a long period of time, and had them hanging close to the surface where the oxygen level was marginally higher. Over the weekend a strong cold front came through, accompanied by rain which suddenly dropped the lake surface water temperature by several degrees. This would have been enough to shock the already stressed fish and make them susceptible to the disease, which is known both to spread rapidly and to kill rapidly. Young fish are particularly sensitive to columnaris. By Friday the lake temperature had dropped enough to knock out all but a residual remnant of the bacteria.

Part of the record high count of herring gulls on May’s Lake, drawn by the bounty.

Don pointed out that there had been two recent years of high bluegill reproduction in May’s Lake, resulting in so many young fish that there was the danger of an overcrowded, stunted population. Consequently, this fish kill may have been a blessing in disguise. Certainly to the many predators with full bellies, it was a great boon.

Vertebrate Miscellany

by Carl Strang

Today, a few vertebrate notes from Mayslake Forest Preserve last week. The redtail youngster still is around.

Though it mainly sits perched in trees or, in this case, on a light fixture, calling frequently, occasionally it changes locations.

One skillful fisherman pulled a nice largemouth from May’s Lake despite the heat.

The bass looked to be 2 pounds or so. The man was fishing early in the morning.

Another example of fishing success was provided by a great blue heron in the stream corridor marsh.

The question is, what was the prey?

The bird was way over on the other side of the marsh. The prey was floppy when the heron shook it, shiny and smooth from the reflected light, and somewhat elongate and irregular in shape at times as the bird shifted its catch. My impression, supported by the dark color (though it was somewhat backlit) is that the prey was a bullhead, which is news because I didn’t think there were any fish in that marsh. The other possibility is a frog, which might better fit certain irregularities in its shape. I’m left with some uncertainty on this one.

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