Friday, February 25, 2005

251: Spelling Out the Causes of Dyslexia -- Vogel 2005 (222): 1 -- sciencenow

Spelling Out the Causes of Dyslexia -- Vogel 2005 (222): 1 -- sciencenow:

Now, researchers believe that they are one step closer to fingering a possible culprit. Natalie Cope and Julie Williams of Cardiff University in the United Kingdom and their colleagues studied 223 people with dyslexia, as well as their families and 273 controls. The team reports in the current issue of the American Journal of Human Genetics that those with dyslexia had a strong tendency to carry alterations in KIAA0319, a gene on chromosome 6p.
This is an evolutionary hypothesis about the relationships of the 273 people and their common descent. The same methods are used to compare mice and flies.

250: Genome of Deadly Amoeba Sequenced -- Inman 2005 (224): 2 -- sciencenow

Genome of Deadly Amoeba Sequenced -- Inman 2005 (224): 2 -- sciencenow:

Entamoeba histolytica infects up to 50 million people worldwide and causes amoebiasis--debilitating diarrhea and liver damage that kills an estimated 100,000 people per year. Among parasitic diseases, amoebiasis is second only to malaria in the numbers it affects and kills. Unlike other amoeba, which possess several types of intracellular compartments called organelles, E. histolytica contains only simple forms of two common organelles, the Golgi apparatus and endoplasmic reticulum. It also lacks the energy-generating mitochondria present in most living things and digests food with fermentation enzymes found only in bacteria and other very simple single-celled organisms. But researchers weren't sure if these were signs that the amoeba was primitive or if it had merely degenerated because of its parasitic lifestyle.

The complete genome of E. histolytica clears up the picture and offers some surprises. Led by scientists at The Institute for Genomic Research (TIGR) in Rockville, Maryland, and the Wellcome Trust Sanger Institute in the United Kingdom, the study indicates that the amoeba has snagged an astonishing 92 genes from bacteria in recent times, presumably by gobbling them up during its life in the human gut. A majority of these genes are involved in metabolism and presumably allow the amoeba to use bacterial metabolic pathways to adapt to the low oxygen environment of the gut. As a result, the amoeba could afford to loose its complex organelles.
Evolutionary hypotheses tested, and 100,000 people a year could be kept alive.

249: Controversy over Flores fossils, Science 307 (5713): 1179

Science -- Culotta 307 (5713): 1179:

Some anthropologists think Homo floresensis is a descendant of Homo erectus, others think it's a microcephalic Homo sapiens. In either event, they study it in the context of evolutionary theories.

More at Zimmer's.

248: Coyne (2005) Ernst Mayr. Science 307 (5713): 1212

Science -- Coyne 307 (5713): 1212:

Mayr nevertheless solved a major problem that eluded Darwin: the origin of biodiversity. Despite the title of his greatest work, Darwin made little contribution to understanding the origin of species. Rather, he explained the origin of features within species. Although others contributed to explaining how new species arise, Mayr and Dobzhansky get the most credit for synthesizing and revitalizing studies of speciation.

247: Solomon et al. (2005) New Perspectives on Ancient Mars. 307 (5713): 1214

Science -- Solomon et al. 307 (5713): 1214:

What is emerging from a better understanding of the early history of Mars is that the Noachian was a time when hydrothermal systems capable of fostering organic synthesis and sustaining any life forms that may have occupied such niches were wide-spread and may have extended at least halfway to the base of the crust.
Remote sensing, recovered Martian meteorites, and Mars rovers, document the geological history of Mars, and uncover the possible early conditions of life on Mars. This is possible because geologists, exobiologists and astronomers rely on evolutionary biology to guide them.

246: Mota et al. (2005) Bacterial Injectisomes: Needle Length Does Matter. Science 307 (5713): 1278

Science -- Mota et al. 307 (5713): 1278:

We found that a minimal needle length was required for efficient functioning of the Yersinia enterocolitica injectisome. This minimal needle length correlated with the length of the major adhesin at the bacterial surface. The needle may be required for triggering type III secretion, and its length may have evolved to match specific structures at the bacterial and host cell surfaces.

245: Zhu et al. (2005) The Selective Cause of an Ancient Adaptation. Science 307 (5713): 1279

Science -- Zhu et al. 307 (5713): 1279:

Phylogenetic analysis reveals that the use of nicotinamide adenine dinucleotide phosphate (NADP) by prokaryotic isocitrate dehydrogenase (IDH) arose around the time eukaryotic mitochondria first appeared, about 3.5 billion years ago.
Then they did an experiment showing how the evolution of NADP use occurred.

244: Stokin et al. (2005) Axonopathy and Transport Deficits Early in the Pathogenesis of Alzheimer's Disease. Science 307 (5713): 1282

Science -- Stokin et al. 307 (5713): 1282:

We identified axonal defects in mouse models of Alzheimer's disease that preceded known disease-related pathology by more than a year; we observed similar axonal defects in the early stages of Alzheimer's disease in humans.
Evolution, helping cure Alzheimer's disease.

243: Thompson et al. (2005) Genotypic Diversity Within a Natural Coastal Bacterioplankton Population. Science 307 (5713): 1311

Science -- Thompson et al. 307 (5713): 1311:

Ecological considerations suggest that much genotypic and possibly phenotypic variation within natural populations should be considered neutral.
That is, a product of random evolution, without significant selection.

242: He Thinks He's People

Science - He Thinks He's People:

Gosling's results indicate that although each species may have its own unique characteristics, fundamental traits are so universal that it's possible to describe humans and animals through terminology designed for either. For example, “openness” in humans is better characterized as “curiosity” in animals. And he found that the traits of neuroticism, agreeableness, and extraversion cut across all species. “Personality ratings are as predictive in dogs as in humans,” says Gosling. He believes that a more thorough understanding of animal personalities can aid research in humans by facilitating the hunt
for biological and genetic bases of personality.

There you go. Common descent of personality.

241: West et al. (2005) Optimization of Virulence Functions Through Glucosylation of Shigella LPS. Science 307 (5713): 1313

Science -- West et al. 307 (5713): 1313:

Thus, LPS glucosylation promotes bacterial invasion and evasion of innate immunity, which may have contributed to the emergence of serotype diversity in Shigella
Understanding the biochemistry of bacteria explains the diversity of dysentery.

Thursday, February 24, 2005

240: Couzin (2005) DNA Tells Story of Heart Drug Failure. Science 307(5713): 1191

Science -- Couzin 307 (5713): 1191:
A single mutation in a receptor protein increases the risk of heart disease and, when placed in mice, makes a beta blocker more effective at treating heart disease.

239: Roosild et al. (2005) NMR Structure of Mistic, a Membrane-Integrating Protein for Membrane Protein Expression. Science 307 (5713): 1317

Science -- Roosild et al. 307 (5713): 1317:

A membrane bound protein which self assembles in the membrane. When another protein is attached to it, the other protein can assemble in-membrane as well. This may imply an early mechanism for moving proteins into bacterial cell membranes, and there are many applications in various forms of biological and evolutionary research.

238: Chih et al. (2005) Control of Excitatory and Inhibitory Synapse Formation by Neuroligins. Science 307 (5713): 1324

Science -- Chih et al. 307 (5713): 1324:

Research on rats shows how the brain develops. If anything were magically designed, it would be the brain, but human brains work the same way.

236: Condon et al. (2005) U-Pb Ages from the Neoproterozoic Doushantuo Formation, China. Science

U-Pb Ages from the Neoproterozoic Doushantuo Formation, China:
Ancient animal fossils are dated at slightly less than 580 million. This times various evolutionary branching points.

235: Life on earth tells us about life on Mars

Creatures Frozen for 32,000 Years Still Alive:

A new type of organism discovered in an Arctic tunnel came to life in the lab after being frozen for 32,000 years.

The deep-freeze bacteria could point to new methods of cryogenics, and they are the sort of biology scientists say might exist on Mars and other planets and moons.
Why should Martian life be like terrestrial life? Because the natural processes that produced life here are operating elsewhere. Evolution proceeds from simple mathematical and logical arguments, and those principles apply everywhere.

Wednesday, February 23, 2005

234: Evolutionary responses to water stress

Water status and leaf elongation of C3- and C4 grasses of Flooding Pampa grassland

The two kinds of grasses evolved to handle water differently at a cellular level. By comparing their responses to water stress, it's possible to factor out evolutionary history and look at raw competitive ability.

233: Pyšek, et. al (2004) Trends in species diversity and composition of urban vegetation over three decades. J. Veg. Science 15(6)

Trends in species diversity and composition of urban vegetation over three decades. The diversity of plants and their responses to urbanization has a genetic (ie. evolved) component.

240: Sexual banter

Sexual banter in workplace may have its benefits | Science Blog:

Sexualized encounters in some work situations actually can contribute to building camaraderie in a workforce, according to a new study by a University of Washington, Bothell, sociologist who examines sexual banter and power in the workplace.
Given that our closest evolutionary relatives in the animal world use sex itself as a tool of social cohesion, this isn't at all surprising.

233-239: Even more Mars

Life on Mars? New Data Reveal Places to Search | Science Blog:

Mars Express, Europe's first mission to the Red Planet, has generated a slew of new data about the mineral composition of the planet's dry, dramatic surface. In six new papers published online by the journal Science, an international team reveals clues about the planet's past hidden in the rock.

Brown University geoscientist John Mustard co-authored three of the Mars papers, currently published on the Science Express Web site. Mustard said this research shows areas that contain water or may have otherwise been amenable to life forms millions of years ago.
We've discussed Mars before.

Tuesday, February 22, 2005

232: Nekola (2004), Vascular plant compositional gradients within and between Iowa fens. J. Veg. Science 15(6)

Vascular plant compositional gradients within and between Iowa fens:

Question: What is the nature and relative importance of compositional gradients within- and between fens?

Conclusions: While the principal axis of variation (corresponding to the rich-poor fen gradient) is present largely between sites, the second axis (corresponding to water level) is largely repeated within sites.
What does this mean? The species in nutrient rich areas are different from poor areas, and that's because some species are adapted (evolutionarily) to different environments.

231: Using evolution to find new drugs

Taxol Pioneer Calls for Greater Emphasis on Natural Products Research | Science Blog:

The RTI International researcher credited with discovering the cancer-fighting drug Taxol is calling for greater investment in natural products research following the discovery reported last month that Taxol slows the spread of Alzheimer’s disease. Dr. Mansukh C. Wani, who with his co-investigator the late Dr. Monroe E. Wall identified and published the structure of Taxol in 1971, said the scientific community is "simply not doing enough research related to natural compounds and as a consequence could be delaying discoveries."

"Less than one-tenth of the world’s plant species have been assessed for pharmaceutical potential," Wani said. "Natural products research is a much longer-term investment, but the potential for finding new ways to treat disease -- and not just one disease as we have seen in the Taxol case -- is enormous."
Which species would you look at first? The ones whose relatives were most pharmacologically active. Why? Because they share evolutionary novelties that produce drugs.

227-230: Micropaleontology 48(4)

Micropaleontology 48/4:

Upper Cretaceous diatom biostratigraphy of the Arctic archipelago and northern continental margin, Canada. Pedro M. Tapia and David M. Harwood, pages 303–342.

Dating the evolution of diatoms (diatoms are important).

Latest Guadalupian (Middle Permian) conodonts and foraminifers from West Texas. Lance L. Lambert, Bruce R. Wardlaw, Merlynd K. Nestell, and Galina P. Nestell, pages 343–364.

Transitional fossils.

Eocene ostracode faunas from the Negev, southern Israel: Taxonomy, stratigraphy and paleobiogeography. A. Honigstein, A. Rosenfeld, and C. Benjamini, pages 365–389.

New fossil species and their evolution.

Paleobiogeography of Maastrichtian to early Eocene Ostracoda of North and West Africa and the Middle East. Ashraf M. T. Elewa, pages 391–398.

Biogeography, migrations and evolution of fossil ostracods (crustaceans).

204-226: Journal of Vertebrate Paleontology 24(3)

Journal of Vertebrate Paleontology 24/3:

New fossil osteoglossomorph from Ningxia, China. Zhang Jiang-Yong, pages 515–524.

Evolution of fossil fish.

A new pycnodont fish genus (Neopterygii: Pycnodontiformes) from the Cenomanian (Upper Cretaceous) of Mount Lebanon. Jürgen Kriwet, pages 525–532.

Evolutionary relationships of fossil fish.

Cranial anatomy and relationships of Microposaurus casei, a temnospondyl from the Middle Triassic of South Africa. Ross Damiani, pages 533–541.

Re-examining a fossil reveals new data about the evolution of this dinosaur.

Description of the skull of a ctenochasma (Pterosauria) from the latest Jurassic of eastern France, with a taxonomic revision of European Tithonian Pterodactyloidea. Stephane Jouve, pages 542–554.

Evolution and ontogeny of pterodactyls.

Growth in small dinosaurs and pterosaurs: The evolution of archosaurian growth strategies. Kevin Padian, John R. Horner, and Armand de Ricqlès, pages 555–571.

Testing an evolutionary hypothesis about the evolution of large size in dinosaurs, birds and mammals.

Description of Prenoceratops pieganensis gen. et sp. nov. (Dinosauria: Neoceratopsia) from the Two Medicine formation of Montana. Brenda Chinnery, pages 572–590.

Evolution of the early horned dinosaurs.

Morphometric analysis of evolutionary trends in the ceratopsian postcranial skeleton. Brenda Chinnery, pages 591–609.

Agreement between phylogeny of horned dinosaurs based on skull and skeleton morphology.

A new Late Cretaceous gavialoid crocodylian from eastern North America and the phylogenetic relationships of thoracosaurs. Christopher A. Brochu, pages 610–633.

A new species and genus of crocodylians, and its evolutionary relationships.

Bone histology and growth patterns of some nonmammalian therapsids. Sanghamitra Ray, Jennifer Botha, and Anusuya Chinsamy, pages 634–648.

Understanding the biology of the reptiles ancestral to mammals.

A new tritylodontid from the Upper Jurassic Shishugou formation of the Junggar Basin (Xinjiang, NW China). Michael W. Maisch, Andreas T. Matzke, and Ge Sun, pages 649–656.

One of the last non-mammalian therapsid fossils. We're talking transitional fossils.

Quantitative analyses of biogeography and faunal evolution of Middle to Late Eocene mammals in East Asia. Takehisa Tsubamoto, Masanaru Takai, and Naoko Egi, pages 657–667.

Macroevolutionary patterns and the impact of the environment on diversity (speciation and extinction).

A new species of nambaroo (Marsupialia: Macropodoidea) from the Miocene Camfield beds of northern Australia with observation on the phylogeny of the Balbarinae. Leah R. S. Schwartz and Dirk Megirian, pages 668–675.

The evolution of kangaroos.

A new large ctenodactylid species from the lower Miocene of Turkey. Raquel López-Antoñanzas, Sevket Sen and Gerçek Saraç, pages 676–688.

The evolution of gundis based on fossil and modern species.

Functional-adaptive analysis of the postcranial skeleton of a Laventan borhyaenoid, Lycopsis longirostris (Marsupialia, Mammalia). Christine Argot, pages 689–708.

By comparing fossil carnivorous marsupials to modern marsupials, the hunting strategies of the fossil species can be inferred. Why? Common descent and parallel evolution.

Bassariscus and Probassariscus (Mammalia, Carnivora, Procyonidae) from the early Barstovian (Middle Miocene). Jon A. Baskin, pages 709–720.
Fossils from the family including coatis and raccoons reveals that one fossil genus is the most similar to the earliest procyonids, while another is more closely related to raccoons.

Late Miocene Promephitis (Carnivora, Mephitidae) from China. Xiaoming Wang and Zhanxiang Qiu, pages 721–731.

The evolution of skunks.

A new giant porcupine (Rodentia, Erethizontidae) from the Late Miocene of Argentina. Adriana Magdalena Candela, pages 732–741.

Fossil porcupine in its evolutionary context.

Further consideration of the earliest known lamprey, Hardistiella montanensis Janvier and Lund 1983, from the Carboniferous of Bear Gulch, Montana, U.S.A. Philippe Janvier, Richard Lund, and Eileen D. Grogan, pages 742–743.

New fossil lampreys show that the sucker existed early in their evolution, and clarifies their early life histories and size.

New material of the mosasaur Carinodens belgicus from the Upper Cretaceous of the Netherlands. Anne S. Schulp, John W. M. Jagt, and Frans Fonken, pages 744–747.

A new fossil reveals the diet of extinct swimming reptiles, and clarifies their evolution.

A new symmetrodont from the Early Cretaceous of England. Pamela Gill, pages 748–752.

A new fossil clarifies the evolution of novel teeth shapes in early mammals.

An oligocene sciurid from the Hsanda Gol formation, Mongolia. Bolortsetseg Minjin, pages 753–756.

A new squirrel fossil is the oldest in Asia, which gives new data on the evolution and spread of squirrels.

A new species of Petromus (Rodentia, Hystricognatha, Petromuridae) from the early Pliocene of South Africa and its paleoenvironmental implications. Frank Sénégas, pages 757–763.

A fossil helps clarify the evolutionary relationships among modern rodents.

From dinosaurs to Dyrosaurids (Crocodyliformes): Removal of the post-Cenomanian (Late Cretaceous) record of Ornithischia from Africa. Matthew C. Lamanna, Joshua B. Smith, Yousry S. Attia, and Peter Dodson, pages 764–768.

New research clarifies evolutionary relationships of a specimen, which has broader implications for biogeography and evolution.

192-203: Paleobiology 31(1)

Paleobiology 31/1:

The importance of museum collections in paleobiology. Warren D. Allmon, pages 1–5.

Among other things, museum collections are valuable because they allow morphological studies. “Morphological studies are crucial bases for evolutionary conclusions at a wide variety of temporal and taxonomic scales and would be impossible (logistically and/or economically) without existing collections.”

Pulsed origination and extinction in the marine realm. Michael Foote, pages 6–20.

That's origination of new species.

Estimating paleodiversities: a test of the taxic and phylogenetic methods. Abigail Lane, Christine M. Janis, and J. John Sepkoski Jr., pages 21–34.

Evolution and speciation.

The morphological diversification of carnivores in North America. Gina D. Wesley-Hunt, pages 35–55.

Evolution and speciation. Gina's cool.

Were there pack-hunting canids in the Tertiary, and how can we know?. Ki Andersson, pages 56–72.

By examining the morphology of fossil canids, Andersson shows that the certain extinct sub-families are more similar to solitary hunting felines, and may have hunted similarly, unlike the pack hunting now common in canids. Evolutionary adaptation and common descent combine to tell us about the behavior of species we never saw.

Early Jurassic climate change and the radiation of organic-walled phytoplankton in the Tethys Ocean. Bas van de Schootbrugge, Trevor R. Bailey, Yair Rosenthal, Miriam E. Katz, James D. Wright, Kenneth G. Miller, Susanne Feist-Burkhardt, and Paul G. Falkowski, pages 73–97.

The macroevolutionary patterns behind the evolution of dinoflagellates correlate with the opening of the ancient Paleopacific to Tethys, the ocean which came to surround the planet, and other tectonic events.

Faunal invasions as a source of morphological constraints and innovations? The diversification of the early Cardioceratidae (Ammonoidea; Middle Jurassic). Nicolas Navarro, Pascal Neige, and Didier Marchand, pages 98–116.

What is the course of morphological evolution and diversification?

Patterns of segregation and convergence in the evolution of fern and seed plant leaf morphologies. C. Kevin Boyce, pages 117–140.

Evolution of leaf shapes.

Contrasting seasonal patterns of carbon gain in evergreen and deciduous trees of ancient polar forests. Dana L. Royer, Colin P. Osborne, and David J. Beerling, pages 141–150.

The conditions of ancient forests and their evolutionary effects is impossible to observe, so they did an experiment by elevating carbon dioxide in a forest. They used closely related species for the most accurate comparison. Common descent = evolution.

Arm regeneration in Mississippian crinoids: evidence of intense predation pressure in the Paleozoic?. Forest J. Gahn and Tomasz K. Baumiller, pages 151–164.

Predation drives theories about the evolution of extinct species. By examining damage and regeneration of ancient crinoid arms, we can learn about predation and its evolutionary importance in the past.

Probable Proterozoic fungi. Nicholas J. Butterfield, pages 165–182.

The oldest known fungi. They share certain distinct characters with modern fungi.

Monday, February 21, 2005

189-191: Proceeding of the Academy of Natural Sciences of Philadelphia

Proceedings of the Academy of Natural Sciences of Philadelphia 154/1:Comparative morphology of the mouthparts, chelipeds and foregut of two kalliapseudid apseudomorphans (Crustacea: Tanaidacea). David T. Drumm, pages 137–147.

The mouthparts of the malacostracan crustaceans are different because they eat different things. Their guts are almost identical because they have a common ancestor.

A new species of the diatom genus


(Bacillariophyceae) from the United States. Eduardo A. Morales and My Le, pages 149–154.

New species put in an evolutionary context.

The taxonomy of the diatom

Lacunicula sardiniensis

Lange-Bertalot, Cavacini, Tagliaventi et Alfinito and its relationship with the genus


Grunow (Bacillariophyceae). Eduardo A. Morales and My Le, pages 155–161.

Evolution of diatoms. Diatoms make good soil, as well as commercial abrasives, including toothpaste.

176-188: Systematic Botany 28(4)

Let's just look at the titles from Systematic Botany 28/4:

Ecological Speciation: Lessons From Invasive Species. Donald A. Levin, pages 643–650.

Studying macroevolution in invasive species (weeds).

Patterns of Molecular and Morphological Variation in Leucobryum albidum, L. glaucum, and L. juniperoideum (Bryopsida). Alain Vanderpoorten, Sandra Boles, and A. Jonathan Shaw, pages 651–656.

Evolution in mosses.

Phylogenetics of Pinus Subsections Cembroides and Nelsoniae Inferred from cpDNA Sequences. David S. Gernandt, Aaron Liston, and Daniel Piñero, pages 657–673.

Phylogenetics = macroevolution. Pine trees.

A Taxonomic Revision of the Eastern North American and Eastern Asian Disjunct Genus Brachyelytrum (Poaceae): Evidence from Morphology, Phytogeography and AFLPs. Jeffery M. Saarela, Paul M. Peterson, Robert J. Soreng, and Ralph E. Chapman, pages 674–692.

Evolution of grasses.

Phylogenetic Relationships of the Afro-Malagasy Members of the Large Genus Begonia Inferred from trnL Intron Sequences. Vanessa Plana, pages 693–704.

Evolution of begonias.

Molecular Evidence for Definition of Genera in the Oxylobium Group (Fabaceae: Mirbelieae). Michael D. Crisp and Lyn G. Cook, pages 705–713.

Evolution of some pea plants.

Resolution of the Galphimia langlassei Complex (Malpighiaceae) from the Pacific Slope of Mexico. Christiane Anderson, pages 714–722.

Understanding the evolutionary relationships between these plants.

Paraphyly of Tarasa (Malvaceae) and Diverse Origins of the Polyploid Species. Jennifer A. Tate and Beryl B. Simpson, pages 723–737.

How polyploidy evolves in different species, and understanding evolutionary relationships.

A Cladistic Analysis of Adelobotrys (Melastomataceae) Based on Morphology, with Notes on Generic Limits within the Tribe Merianieae. Leif Schulman and Jaakko Hyvönen, pages 738–756.

Cladistics = phylogenetics = evolution.

Cornus eydeana (Cornaceae), A New Cornelian Cherry from China—Notes on Systematics and Evolution. (Jenny) Qiu-Yun Xiang, Yu-Min Shui, and Zack Murrell, pages 757–764.

Evolution of a cherry.

A Revision of Nasa ser. Carunculatae (Loasaceae subfam. Loasoideae). Maximilian Weigend, Tilo Henning, and Christof Schneider, pages 765–781.

Evolution of these plants.

Inferred Phylogeny in Keckiella (Scrophulariaceae) based on Noncoding Chloroplast and nuclear ribosomal DNA Sequences. C. Edward Freeman, J. Scott Harrison, John P. Janovec, and Ron Scogin, pages 782–790.

More evolution of plants.

Classification of Convolvulaceae: A Phylogenetic Approach. Saša Stefanovi, Daniel F. Austin, and Richard G. Olmstead, pages 791–806.

Using evolution to classify plants like sunflowers, asters, daisies, etc.

173-175: Transactions of the Kansas Academy of Science 107(3)

Mike Engel reviews the systematics of (and evolutionary connections among) The alderflies of Kansas (Megaloptera: Sialidae).

Michael J. Everhart and Michelle K. Darnell describe the Occurrence of Ptychodus mammillaris (Elasmobranchii) in the Fairport Chalk Member of the Carlile Shale (Upper Cretaceous) of Ellis County, Kansas. These are fossils from the sea that covered Kansas eons ago.

More fossils, this time from Kenshu Shimada, Keith Ewell, and Michael J. Everhart. They offer The first record of the lamniform shark genus, Johnlongia, from the Niobrara Chalk (Upper Cretaceous), western Kansas. That's a new fossil species of shark.

You can bet money these folks are doing this because they want to understand evolution.

172: Insect smelling

'Blinding' an insect's sense of smell may be the best repellent | Science Blog:

The researchers studied four very different insect species: a benign insect favored by researchers, the fruit fly, which is attracted to rotting fruit, and three pest insects: the medfly, which is a citrus pest; the corn earworm moth, which damages corn, cotton and tomato crops; and the malaria mosquito, which targets humans. They found that one gene, shown to be responsible for the sense of smell in fruit flies, has the same function in these pest insects, which are separated by over 250 million years evolution

“While all these insects have sensitive olfactory systems, they all have very different smell preferences,” says Vosshall, head of the Laboratory of Neurogenetics and Behavior. “Yet this odorant receptor is highly conserved across all of these different species.”
Hmm. Evolutionary hypothesis leads to an experiment. The results show common descent, and reveals a means of preventing mosquitoes from noticing people, agricultural pests from noticing fruit, etc.

171: Mars again!

New Scientist Breaking News - 'Pack ice' suggests frozen sea on Mars:

In their paper, the researchers trace a possible history for the underground ice. It begins with huge masses of ice floating in water on Mars. The ice was later covered with volcanic ash, preventing it from sublimating away into the thin atmosphere. Then, the ice broke up and drifted before the remaining liquid water froze. All of the ice not protected by ash sublimated away, leaving the pack ice plates behind.

"If the reported hypothesis is true, then this would be a prime candidate landing site to search for possible extant life on Mars," says Brian Hynek, a research scientist at the Laboratory for Atmospheric and Space Physics at the University of Colorado at Boulder, US.
We only care about where water is because naturalistic and evolutionary science tell us that life is most likely to occur near water. These are weak predictions. Life can probably exist in the absence of water, and water exists in the absence of life, but they seem to go together. Evolution will help us find life on Mars, if it's there.

170: More on Mars

This is a nice discussion of the ways that evolutionary biology informs NASA's exploration of space: Would Methane on Mars Mean Life? | Science Blog

It's a subject of great interest to me.

Sunday, February 20, 2005

156-169: The rest of Evolution 59:1

Countergradient variation in the sexual coloration of guppies (Poecilia reticulata): Dropsopterin synthesis balances carotenoid availability:

Limits on carotenoids in the diet force guppies to vary the amount of dropsopterin they produce. The ratio is constant across regions, so the populations may have evolved different levels of dropsopterin in response to environmental carotenoid levels. Genetic studies show that dropsopterin levels are genetically controlled. Evolution produced a testable hypothesis and that hypothesis leads to new research on mechanisms of speciation (macroevolution).

Ecological adaptation and species recognition drives vocal evolution in neotropical suboscine birds:

Evolutionary differences in mating signals, as regularly discussed here, plays a major role in speciation. The authors evaluate various hypotheses about mating system divergence, and test three. They found that closely related species living together are more divergent in song than species living apart. The environment and body size also had a significant influence on songs.

Testable predictions come from evolutionary hypotheses, and the results yield more macroevolutionary hypotheses.

Fine scale endemism on coral reefs: Archipelagic differentiation in turbinid gastropods:

Here we show that the gastropod Astralium “rhodostomum” has developed endemic clades on almost every Pacific archipelago sampled, a pattern unprecedented in marine biogeography, and reminiscent of the terrestrial biota of oceanic islands. Mitochondrial DNA sequences indicate that this species-complex is comprised of at least 30 geographically isolated clades, separated by as little as 180 km. Evidence suggests that such fine scale endemism and high diversity is not exceptional, but likely characterizes a substantial fraction of the reef biota. These results imply that (1) marine speciation can regularly occur over much finer spatial scales than generally accepted, (2) the diversity of coral reefs is even higher than suggested by morphology-based estimates, and (3) conservation efforts need to focus at the archipelagic level in the sea as on land.
New evolutionary hypotheses are tested and we increase our understanding of evolution, speciation, diversity, and conservation.

Geographical variation in the rate of evolution: Effect of available energy or fluctuating environment?

Responding to a previous article, the authors feel that the tests of an evolutionary hypothesis were insufficient. Evolution leads to testable hypotheses and allows for disagreements.
Growth rate correlates to individual heterozygosity in the European eel, Anguilla anguilla L:

We provide evidence for a positive correlation between genetic variability and growth rate at 12 allozyme loci in a catadromous marine fish species, the European eel (Anguilla anguilla L.). More heterozygous individuals show a significantly higher length and weight increase and an above average condition index in comparison with more homozygous individuals.
That means genetic diversity is being selected for in these species. Evolutionary hypotheses tested.

Increased rates of molecular evolution in an equatorial plant clade: An effect of environment or phylogenetic nonindependence?

Why do equatorial Mearnsia have more rapid molecular evolution than more southerly congeners? The authors disagree with a previous paper which argued for the effect of geography. This paper finds that the effect can be explained by the common descent of the equatorial clade.

Male-by-female interactions influence fertilization success and mediate the benefits of polyandry in the sea urchin Heliocidaris erythrogramma:

Numerous studies have reported that females benefit from mating with multiple males (polyandry) by minimizing the probability of fertilization by genetically incompatible sperm. Few, however, have directly attributed variation in female reproductive success to the fertilizing capacity of sperm. In this study we report on two experiments that investigated the benefits of polyandry and the interacting effects of males and females at fertilization in the free-spawning Australian sea urchin Heliocidaris erythrogramma
Polyandry is an evolved pattern in urchins. Evolution produces testable hypotheses.

Polyandry promotes enhanced offspring survival in decorated crickets

Is a theme developing? Multiple matings in crickets mean that females leave more offspring and that those offspring survive longer. Evolutionary theory predicts that polyandry would be common under these circumstances, and it's true.

Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes:

Here we discriminate between two competing hypotheses with a molecular phylogeography dataset comprising approximately 4800 bp of mtDNA and demonstrate that populations of island dwarfs and giants have evolved five times independently. In each case the closest relatives of the giant or dwarf populations are mainland tiger snakes, and in four of the five cases, the closest relatives are also the most geographically proximate mainland tiger snakes. Moreover, these body size shifts have evolved extremely rapidly and this is reflected in the genetic divergence between island body size variants and mainland snakes.
In addition to the tests of evolutionary hypotheses, and the documentation of the process behind speciation, we also get insight into why some snakes get bigger, and others smaller. Small snakes are on islands with small prey, big snakes on islands with big food. This is called character displacement, a testable evolutionary hypothesis.

Rates of divergence in gene expression profiles of primates, mice, and flies: Stabilizing selection and variability among functional categories

By comparing two strains of lab mice, two species of fruit fly, and humans and chimps, the authors show that while genes diverge, the expression of genes is constant across time. This implies directional selection, and the divergence can be explained by short periods of directional selection. That's a lot like Gould and Eldridge's punctuated equilibrium.

Sexual selection, genetic architecture, and the condition dependence of body shape in the sexually dimorphic fly Prochyliza xanthostoma (Piophilidae)

Sexual selection explains why certain characteristics of the flies respond highly to the fly's body condition, in accordance with theory.

The probability of parallell evolution:
More precisely, what is the probability that selection will cause two populations that live in identical environments to substitute the same beneficial mutation? Here I show that, under fairly general conditions, the answer is simple: if a wild-type sequence can mutate to n different beneficial mutations, replicate populations will on average fix the same mutation with probability P = 2/(n + 1).
Evolution inspires novel and testable hypotheses.

The role of Haldane's rule in sex allocation:

Sex allocation theory predicts that parents should bias their reproductive investments toward the offspring sex generating the greatest fitness return. When females are the heterogametic sex (e.g., ZW in butterflies, some lizards, and birds), production of daughters is associated with an increased risk of offspring inviability due to the expression of paternal, detrimental recessives on the Z chromosome. Thus, daughters should primarily be produced when mating with partners of high genetic quality. When female sand lizards (Lacerta agilis) mate with genetically superior males, exhibiting high MHC Class I polymorphism, offspring sex ratios are biased towards daughters, possibly due to recruitment of more Z-carrying oocytes when females have assessed the genetic quality of their partners. If our study has general applicability across taxa, it predicts taxon-specific sex allocation effects depending on which sex is the heterogametic one.
And why would the pattern hold? Evolutionary theory and common descent.

The transition to social inbred mating systems in spiders: Role of inbreeding tolerance in a subsocial predecessor:

The social spiders are unusual among cooperatively breeding animals in being highly inbred. In contrast, most other social organisms are outbred owing to inbreeding avoidance mechanisms. The social spiders appear to originate from solitary subsocial ancestors, implying a transition from outbreeding to inbreeding mating systems. Such a transition may be constrained by inbreeding avoidance tactics or fitness loss due to inbreeding depression. We examined whether the mating system of a subsocial spider, in a genus with three social congeners, is likely to facilitate or hinder the transition to inbreeding social systems. … It is likely that the lack of inbreeding avoidance in subsocial predecessors has facilitated the transition to regular inbreeding social systems.
Evolution generates testable hypotheses about macroevolutionary transitions, and their predictions are borne out.

Next up: The Journal of Mammalogy, or maybe Ecology.

Saturday, February 19, 2005

155: Genetic enhancements help clean up soil

news @ - Transgenic mustard sucks up selenium - First field results prove plant can remove soil contaminants.:

Farmland in certain parts of California is heavily irrigated, and the water dissolves selenium in shale found in the region. As the water evaporates on the surface soil, selenium is concentrated to levels that are toxic to plants. But Indian mustard (Brassica juncea) has a natural resistance to the element, and absorbs it as it takes in water through its roots.

"Indian mustard is able to grow fast and attain a high biomass even under environmentally stressful conditions," says Norman Terry, a plant biologist at the University of California, Berkeley, who led the study. The researchers boosted Indian mustard's abilities by adding extra genes that produce selenium-hungry enzymes.
The natural resistance and sequestration of selenium is an evolutionary adaptation to challenging environments. Scientists used that as a starting point to make the mustard more effective. They knew which genes to look at because of the naturally evolved adaptations. Evolutionary hypotheses generate new theories, which rehabilitate polluted farmland.

154: Treating Huntington's disease

Promising treatments for Huntington's disease identified | Science Blog:

"Preclinical testing strategies such as those we used with fruit flies can result in a great savings of cost and time in developing potential disease treatments," Marsh said. "They can serve to rapidly identify treatment regimens that are very likely to provide effective therapeutic benefit to patients."

In developing these drug combinations, Marsh and Thompson chose compounds that individually have been shown in other fruit-fly tests and in mouse models to suppress neurodegeneration, but each targets different cellular processes.
Yada yada yada. Flies and mice tell us about the functioning of human cells because of common descent. Evolution gives us testable predictions.

153: Mice brains tell us about human schizophrenia

Researcher links schizophrenia, gene mutations | Science Blog:

By examining brain tissue from mice with various gene mutations, the researchers determined that the brain appears to compensate for the altered gene by becoming supersensitive to dopamine. Dopamine is a neurotransmitter that allows people to move, think and feel.
Mice, people which is it? Both, thanks to evolution!

152: Using Co-evolution to combat invasive species

Moth Released to Curb Spread of Climbing Fern | Science Blog:

Climbing fern is native to the Old World tropics including Australia, Africa, tropical Asia and the Pacific Islands but doesn't cause problems in those areas, probably because natural enemies help keep it in check. Searching for natural enemies of the fern in its native habitat, scientists at the ARS Australian Biological Control Laboratory in Indooroopilly identified several promising candidates, including A[ustromusotima] camptonozale. Then they tested these biocontrol candidates to make sure they would only feed on the fern and not on other, nontarget plants.
Climbing ferns under control elsewhere because the evolved in a particular ecosystem. Without the predators it evolved a response too, it goes wild. Evolutionary (and ecological) theory predicts how to combat the climbing ferns, introduce a predator it evolved with. Let's hope it works.

151: Better leukemia drugs prevent cancer from evolving

Gleevec is a conventional leukemia treatment. CML is chronic myelogenous leukemia.

Designer drug potent treatment for chronic myelogenous leukemia | Science Blog:

Gleevec shuts down CML by blocking the function of Bcr-Abl, the abnormal tyrosine kinase protein in the leukemic cells that causes them to grow too quickly. However, it does not bind very tightly to this protein, takes a long time to induce remissions, and patients can develop a resistant type of Bcr-Abl that no longer binds to Gleevec at all.

To circumvent these shortcomings, researchers at Novartis determined the crystal structure of Bcr-Abl, and then constructed compounds that would lock into the receptor more securely than Gleevec. Investigators at Dana-Farber tested the new compounds to measure their effectiveness against CML in laboratory cell cultures and mice with the disease.
Why does the leukemia become resistant? Evolution within the body. How did they test the new drug? In animal models. They care about model systems because of evolution.

Friday, February 18, 2005

150: Why Vioxx and Celebrex can be dangerous

COX inhibitors interfere with the action of prostaglandins. Prostaglandins protect the nervous system.

COX-2 product offers good and bad news in 'test tube' strokes | Science Blog:

Andreasson is now trying to determine if these prostaglandins have a similar protective effect in mouse models of Lou Gehrig's disease, in which excessive glutamate is believed to damage neurons, and will begin work to see if the beneficial side of PGD2 activity can outweigh its toxic activity.
Is it trivial to keep pointing to studies that use animal models? No. Animal models are vital to medical science and huge swaths of basic research. No one really gives two shits about Drosophila or Arabidopsis or lab mice. We study them because they are evolutionarily connected to everything else. If everything was magically summoned up, mice would tell us nothing about humans.

Common descent is behind every medicine, every surgical technique, everything. That's what makes this such a tough blog to maintain.

Anyone who wants to help is free to submit interesting stories they see.

149: Comparing recombination in humans and chimps

Researchers interested in recombination compared the areas with frequent crossovers in humans and chimps, expecting that similar genetic codes would produce similar crossover hotspots.

Surprising difference between human and chimp genomes | Science Blog:

They identified 18 hotspots in humans and three hotspots in chimps. To their surprise, none of the hotspots occurred in the same locations in human and chimp.

"The surprising conclusion seems to be that there is probably something other than the DNA sequence, or perhaps in addition to it, that is determining where these hotspots are located," said Altshuler. "Epigenetic factors--biological codes that are layered on top of the DNA--may turn out to be more different in closely related species than the DNA sequence itself."
Why isn't this at The Non-Evolution Project? Because an evolutionary hypothesis generated a testable hypothesis. There are still naturalistic explanations; the story of the genome is just more complicated than it seems at first glance.

Remember, science is a method, not an encyclopedia. A hypothesis that fails is usually more interesting that a successful prediction. It means something interesting happened. It doesn't mean science failed, it means that one hypothesis failed. In this case, the hypothesis was that crossing over was dictated by the genetic sequence at the crossover site. That failed, and it helps explain why humans and chimps aren't identical. Evolution led us to interesting questions, and opened up a new frontier.

148: Evolutionary sleuths identify some UTI causing bacteria

Contaminated food can lead to urinary tract infections in women | Science Blog:

The researchers found that the E.coli causing the UTIs matched genetically with a sample of E.coli obtained from an animal source. They used E.coli samples collected over 40 years from the center to match up the bacteria causing UTIs with bacteria found in animals. They tested E.coli samples from dogs, cows, sheep, water and turkeys. The researchers then compared the samples genetically to the UTI causing bacteria and found that a sample from a cow matched well with the E.coli found in humans.
Expand that. They took the samples, made a phylogeny, and found that the samples from women with urinary tract infections shared the most characters with the samples from cows. E. coli evolves randomly and through selection, like everything else, and these researchers used that to identify the culprit in many infections. Thanks evolution.

147: Resurrecting dead bone

Gene therapy converts dead bone graft to new, living tissue | Science Blog:

Researchers have created a way to transform the dead bone of a transplanted skeletal graft into living tissue in an experiment involving mice. The advance, which uses gene therapy to stimulate the body into treating the foreign splint as living bone, is a promising development for the thousands of cancer and trauma patients each year who suffer with fragile and failing bone grafts. The findings were posted online Feb. 13 and will appear in the March 1 issue of Nature Medicine.
Why are they talking about using results from mice to cure human diseases?

Common descent means evolution means that mice and people are not so different.

146: Safety in numbers

For Some Insects, It's Smart to Run With the Crowd | Science Blog:

The researchers discovered that for the crickets, there's safety in large numbers. Those insects which were part of a large moving band were much less likely to be eaten. In fact, 50 to 60 percent of the Mormon crickets that were separated from a migratory band were killed within two days by predators such as birds and rodents, while none of those staying with the band were eaten. Radio transmitters belonging to those unfortunate, lone insects were found either chewed or still glued to a partially-eaten cricket corpse.
Natural selection at work. Just another day in the exciting world of evolutionary biology. Testable evolutionary hypotheses, and positive results.

144-145: Bacterial evolution

Each new pair of bacteria inherit one end from the parent cell, and produce a new end of their own. The offspring that gets the new end is healthier.

Science -- Editor's Choice {18 February 2005; 307 (5712)}:

Because these asymmetric characteristics are hallmarks of cellular aging in multicellular organisms and in yeast, the study suggests that asymmetric cell division and fundamental mechanisms of aging may be evolutionarily conserved in bacteria.
There's that pesky word again. Can evolution in bacteria explain human aging? Stay tuned!

Also in Science: How bacteria adapt to live in human skin. It's a mechanism also used to avoid the immune system and some antibiotics. Evolution at work.

143: North America's Anatomy

We previously discussed the interaction between tectonic theory and evolution. An updated geological map of North America incorporates new knowledge about plate tectonics to better understand our geology.

141-142: Variation in the human genome

Science -- Hinds et al. 307 (5712): 1072:

Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Our results indicate that these SNPs capture most common genetic variation as a result of linkage disequilibrium, the correlation among common SNP alleles. We observe a strong correlation between extended regions of linkage disequilibrium and functional genomic elements. Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations.
These SNPs have distinct regional patterns because of evolution. There's no other sensible explanation. Understanding them tells us about the evolution of humans and our spread and interbreeding over hundreds of thousands of years.

There's also a nice commentary about "Harvesting Medical Information from the Human Family Tree." Human evolutionary information is a great tool for identifying cryptic genetic diseases.

140: Controlling marrow growth

Science -- Opferman et al. 307 (5712): 1101:

Apoptosis is important in controlling hematopoietic stem cell (HSC) numbers. However, the specific BCL-2 family member(s) that regulate HSC homeostasis are not precisely defined. We tested myeloid leukemia–1 (MCL-1) as an attractive candidate that is highly expressed in HSCs and regulated by growth factor signals. Inducible deletion of Mcl-1 in mice resulted in ablation of bone marrow. This resulted in the loss of early bone marrow progenitor populations, including HSCs. Moreover, growth factors including stem cell factor increased transcription of the Mcl-1 gene and required MCL-1 to augment survival of purified bone marrow progenitors. Deletion of Mcl-1 in other tissues, including liver, did not impair survival. Thus, MCL-1 is a critical and specific regulator essential for ensuring the homeostasis of early hematopoietic progenitors.

While they didn't test this in humans, they only did this because understanding the functioning of mouse stem cells is key to understanding human leukemia. Why does MCL-1 occur in mice and humans? Why do we think it would work the same way in both? Common descent.

What's the point of this? Apoptosis is controlled cell death. Uncontrolled cell growth has a name: cancer.

Evolution is helping to cure cancer.

139: Evolution of rodents and rabbits

Science -- Asher et al. 307 (5712): 1091:

We describe several fossils referable to Gomphos elkema from deposits close to the Paleocene-Eocene boundary at Tsagan Khushu, Mongolia. Gomphos shares a suite of cranioskeletal characters with extant rabbits, hares, and pikas but retains a primitive dentition and jaw compared to its modern relatives. Phylogenetic analysis supports the position of Gomphos as a stem lagomorph and excludes Cretaceous taxa from the crown radiation of placental mammals. Our results support the hypothesis that rodents and lagomorphs radiated during the Cenozoic and diverged from other placental mammals close to the Cretaceous-Tertiary boundary.
Lagomorphs are rabbits, hares, and pikas. This might be referred to as a "missing link" of the rodents. Why do we care? Most mammals are rodents, and this tells us about the evolution of the most successful group of mammals. Cool!

138: Golgi bodies

Science -- Malsam et al. 307 (5712): 1095

Again, I can't quite piece together what's happening here. But it relates to the inner working of cells. Whose cells? Doesn't matter, the authors don't tell us. We know it's eukaryotic, but really not much else. That's because cells are, broadly speaking, cells. They work the same because they all evolved from the same starting point, and that starting point did whatever it is this article is about.

137: Enzymes of some sort

I have no idea what this means, but …

Science -- Sarbassov et al. 307 (5712): 1098:

We show that in Drosophila and human cells the target of rapamycin (TOR) kinase and its associated protein rictor are necessary for Ser473 phosphorylation and that a reduction in rictor or mammalian TOR (mTOR) expression inhibited an Akt/PKB effector.
It works the same way in humans and flies? Common descent.

Anyone care to translate the article to non-molecular?

136: Roach sex pheromones

Science -- Nojima et al. 307 (5712): 1104:

The sex pheromone of the German cockroach, Blattella germanica, has been characterized as gentisyl quinone isovalerate. This cockroach is a major cause of allergic disease and serves as a mechanical vector of pathogens, making it one of the most important residential and food-associated pests worldwide.
Sex pheromones evolve just like cricket calls or rodent penises. Understanding the product of the mechanism that allows roaches to meet each other is key to preventing all manner of diseases.

135: Ancient crocodilian

Yahoo! News - Scientists Unveil Fossilized Crocodile:

“We're learning about a new species of crocodile, the ecosystem of 70 million years ago, and the evolution of the land crocodile on the ancient continent of Gondwana,” Carvalho said.

Scientists believe the continents then were joined in a huge land mass, which some call Gondwana. Fossils similar to Uberabasuchus have been found in Africa and in Antarctica, which possibly were linked to South America.
Evolutionary hypotheses match up with independent geological hypotheses. Plus, we learn a little about ancient crocodiles.

As a side note, Gondwana is the southern super-continent. Laurasia was in the north. Both split from Pangaea, the single landmass that existed 225 million years ago.

Thursday, February 17, 2005

134: Exclusive: NASA Researchers Claim Evidence of Present Life on Mars

Exclusive: NASA Researchers Claim Evidence of Present Life on Mars:

What Stoker and Lemke have found, according to several attendees of the private meeting, is not direct proof of life on Mars, but methane signatures and other signs of possible biological activity remarkably similar to those recently discovered in caves here on Earth.

Stoker and other researchers have long theorized that the Martian subsurface could harbor biological organisms that have developed unusual strategies for existing in extreme environments. That suspicion led Stoker and a team of U.S. and Spanish researchers in 2003 to southwestern Spain to search for subsurface life near the Rio Tinto river—so-called because of its reddish tint—the product of iron being dissolved in its highly acidic water.
The article goes on to describe how evolutionary hypotheses about life on Mars led the team to look for similar conditions on earth. Then, having found life in unexpected places on Earth (click for more on the value of prediction) they looked for new data on Mars. The results they got matched those on Earth.

Evolutionary hypotheses work on every planet, and here's a case where evolution may have given us the first evidence of life on another planet. Too cool.

Starman” by David Bowie from the album The Rise And Fall Of Ziggy Stardust And The Spiders From Mars (1972, 4:13).

133: Zinc-based sulfide-binding mechanism in tubeworms

Novel Sulfide-Binding Mechanism Found in Deep-Sea Tubeworms | Science Blog:

The unusual form of hemoglobin gives the worms an advantage over other organisms competing for space near the vents and may play a role in their ability to adapt to a wide temperature range.
The tubeworms, which grow in the bizarre deep-sea vent environment, have a highly efficient hemoglobin, which carries both sulfide and oxygen. They do this by modifying the hemoglobin proteins into a more stable form than the human version, and integrating zinc to increase the binding points for sulfide and oxygen.

Why not use an entirely new molecule? Because evolution works with what's there. Why don't we have this super-efficient hemoglobin? Perhaps because too much oxygen is a bad thing.

132: Birds' evolve to lay eggs en masse

Darling's hypothesis is that birds in colonies will have earlier, larger, and more synchronized clutches of eggs.

news @ - Social sounds boost bird breeding - Zebra finches base their mating decisions on group consensus.:

To test Darling's hypothesis, the researchers set up two indoor colonies of the zebra finch (Taeniopygia guttata), a smart little Australian bird often seen in pet shops.

The first group of birds was played recorded sounds of its own colony, but the second group heard a playback that blended its own colony sounds with noises from extra finches.

Females in the second group had more eggs, laying them earlier and more synchronously than controls, confirming the theory.

Peter Boag, a biologist at Queen's University in Ontario, Canada, who worked on the study, explains the advantages of this mating pattern. It is probably beneficial for a bird to have its chicks at the same time as the couple on the next nest, he says. With more chicks around, the risk to each individual chick from predators is reduced.

It is also advantageous for a female to start laying early in the season, because this gives her more time to invest in her brood and makes it likely that she will fledge more chicks successfully.

However, laying too early will isolate chicks and put them at risk, so how do females decide when to lay?
Darling proposed an evolutionary hypothesis. People tested it experimentally. It checks out. More questions are raised.

The exact mechanism for the effect is still being worked out, says Boag, but other studies have shown that hearing social sounds can cause changes in hormone levels in birds

131: Producing new vaccines requires getting around evolution

news @ - Potatoes pack a punch against hepatitis B - Plant that contains vaccine shows promise in human trials.:

Unlike travellers' diarrhoea and the Norwalk virus, the hepatitis B virus did not evolve to survive in the gut, which makes the success of this edible vaccine all the more surprising.
After producing potatoes that contain vaccines against E. coli and Norwalk virus, they turned their attention to hepatitis B. But the antigens to hepatitis don't occur in the gut, so it took special effort to get those antigens to move into the bloodstream. Evolution put up roadblocks, science went around.

130: Evolutionary responses to pollutants

news @ - 'Pollutants' in whale blubber are naturally produced - Sea creatures make chemicals similar to those spewed out by human factories.:

Reddy says there are larger implications. "We can start to think about how humans and animals and plants have evolved over millions of years. We've only manufactured these compounds since the 1930s. The way we respond to these compounds might have been programmed over many generations." It might explain, he suggests, why some enzymes in the natural world can break down these kinds of molecules.
A sponge produces chemicals like those produced industrially. Whales accumulate the natural form of the toxin. Scientists immediately look at the evolutionary implications.

129: Using evolved toxins as pesticides

Spider Venom Could Yield Eco-Friendly Insecticides | Science Blog:

One approach is to create chemical insecticides that mimic the action of spider toxins. Many insects have developed immunity to DDT and other chemical controls because most insecticides are neurotoxins that act against only a small number of nervous system targets. King's spider-venom cocktails could be designed to thwart the resistance of specific insect pests by locking on to novel molecular targets in the insect nervous system. Because the insects have never encountered chemicals that behave like spider toxins, they will most likely lack resistance to bioinsecticides derived from funnel-web venom.
Why do we think spider venom would work better? Because venoms that were easy to adapt to were selected against, and resistance to them spread through insect populations. So evolutionary science predicts that naturally occurring venoms should target more highly conserved portions of the nervous system, parts that can't adapt as easily.

Reducing the current loss of 25% of crops to insects: just another day for evolutionary biology.

128: Mouse results on IVF embryos suggest changes in human treatment

IVF embryos may be starved of vital ingredient | Science Blog:

The lack of natural growth factors in the fluid in which IVF embryos are grown could have lifelong effects on people conceived this way. That is the implication of a study on mice by Australian researchers, who say preliminary studies of human embryos back their claims.
Why do we care what happens to mice? Because mice are mammals, like humans, and their physiology isn't so different because of our evolutionary similarities. An evolutionary hypothesis that makes babies healthier.

127: Creationist Confusion about pharyngeal homologies

Pharyngula::Creationist Confusion about pharyngeal homologies:

Gosh, cranial nerve distributions are nearly identical in fish and mammals! There are some interesting differences—cats lack lateral lines and gills, of course, and they are separated by several hundred million years of evoluton—but overall, the similarities are overwhelming.

Alas, poor Serge. He has made three conceptual errors that are trivially refuted, with 20-30 year old sources, no less.
  • His naive expectation that there’d be a one-to-one correspondence between cranial nerves and pharyngeal arches is mistaken. We don’t see such a thing, nor do we expect such a thing.
  • He has the homologies of the pharyngeal arch derivatives out of register. Cranial nerve V does not innervate the first gill, and evolutionary homologies would predict that it shouldn’t innervate the gill.
  • If he thinks the anatomical and functional correlations of the cranial nerves between fish and tetrapods support a creationist model, well, then he should be persuaded otherwise. They line up very, very well, and reflect common descent.
I was tempted to leave this unnumbered, since the sources aren't new. It's just too good to pass up, though.

Thanks, Paul.

104-126: Microbiology roundup

Someone else gets it. I don't plan to read every damn thing. So the incorrigible Mike the Mad Biologist offers Microbiology and Evolution:

Microevolution and history of the plague bacillus, Yersinia pestis, Achtman, et al. (2004) PNAS 101: 17837.
The plague bacillus did not evolve from Yersinia pseudotuberculosis ~1,500 years ago, but instead arose and spread globally >10,000 years ago.

Natural Isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation, Bergthorsson et al. (2005) J. Bacteriol. 187:400.
This article tests various evolutionary hypotheses about why certain disease-causing Salmonella can not synthesize pyridine.

Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes, Winfield et al. (2004) PNAS 101: 17162.
Differences in gene regulation account for phenotypic divergence between Salmonella and E. coli.

Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation, Vinuesa et al. (2005) Molecular Phylogenetics and Evolution 34:29.
“This finding provides strong evidence for the existence of well delineated species in the bacterial world.”

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human, Song et al. (2005) PNAS 102:2430.
Uses evolutionary analyses to determine where the SARS virus came from and what genetic changes made it dangerous to humans.

Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes, Tanabe et al. (2005) PNAS 102:2436.
The MADS-box genes of land plants are extensively diverged to form a superfamily and are important in various aspects of development including the specification of floral organs as homeotic selector genes....These expression patterns suggest that the precursors of land plant MADS-box genes originally functioned in haploid reproductive cell differentiation and that the haploid MADS-box genes were recruited into a diploid generation during the evolution of land plants.“

Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization, Morrell et al. (2005), PNAS 102:2442.
Inbreeding plants appear to have the same lack of linkage disequilibrium as outcrossing plants. If you really want to know why the Mad Biologist finds this very interesting you'll have to send email.

Genomic insights that advance the species definition for prokaryotes, Konstantinidis et al. (2005), PNAS 102:2567.
Compares bacterial species definitions derived from traditional methods to those derived from genome data.

Neutral microepidemic evolution of bacterial pathogens, Fraser et al. (2005). PNAS 102:1968.
”The analysis suggests the emergence of neutral bacterial population structure from overlapping microepidemics within clustered host populations and provides insight into the nature and size distribution of these clusters. These findings challenge the assumption that strains of bacterial pathogens differ markedly in relative fitness.“

A monkey's tale: The origin of Plasmodium vivax as a human malaria parasite, Escalante et al. (2005), PNAS 102:1980.
Human malaria may have evolved from malaria found in Southeast Asian macaques, not from animals in Africa.

A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: The search for the unit of selection, Castillo et al. (2005), PNAS 102:1542.
Recombination and selection may be breaking breaking apart this genomic region so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.

High rate of viral evolution associated with the emergence of carnivore parvovirus, Shackleton et al. (2005), PNAS 102:379.
Carnivore parovirus is a recently emergent virus that kills dogs. Read this article or more puppies will die!

Experimental evolution of conflict mediation between genomes, Sachs et al. (2005), PNAS 102:390.
Using two bacterial viruses, the authors examine the following phenomena: evolution of reduced genomes in symbionts, cotransmission of partners, and obligate coexistence between cooperating species.

Postzygotic isolating factor in sympatric speciation in Rhagoletis flies: Reduced response of hybrids to parental host-fruit odors, Linn et al. (2005), PNAS 101:17753.
Rhagoletis is an excellent example of speciation that we have been able to observe. This paper describes a mechanism by which speciation has happened.

Extensive gene diversity in septicemic Escherichia coli strains, Mokady et al. (2005) J. Clin. Microbiol. 43:66.
This paper shows that there is extensive genome plasticity between E. coli that cause the same disease and target similar tissues. Also, gene associated with virulence are found in a variety of different animals, ”implying a high degree of zoonotic risk.“

The limits of theoretical population genetics, Wakeley (2005), Genetics 169:1.
Gee, what do you think it's about?

Lack of evidence for horizontal transfer of the lac operon into Escherichia coli, Stoebel (2005), Mol. Biol. Evol. 22:683.
The ability to use lactose by E. coli has always been cited as the prime example of horizontal gene transfer giving rise to ecological divergence. Dan blows this example away.

Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii related Shigella boydii strains, Hyma et al. (2005), J. Bacteriol. 187:619.
There's a new species of Escherichia.

Microeconomic principles explain an optimal genome size in bacteria, Ranea et al. (2005), Trends in Genetics 21:21.
Why are bacterial genomes the sizes that they are?

A bunch of fun-guys: the whole-genome view of yeast evolution, Ochman et al. (2005), Trends in Genetics 21:1.
Genome evolution in yeasts is different than genome evolution in bacteria, largely because yeast chromosomes have stronger selective constraints.

Germs, genomes, and genealogies, Wilson et al. (2005), Trends in Ecology and Evolution 20:39.
Pathogen biology can be inferred from patterns of molecular variation.

Weighted genome trees: refinements and applications, Gophna et al. (2005), J. Bacteriol. 187:1305.
How to construct genome-level phylogenies.

I think that's enough to keep you busy...
You bet, Mike. Thanks for the help.

Wednesday, February 16, 2005

103: Earliest human fossils

The New York Times > Science > Oldest Remains of Human Beings Are Identified:

Scientists have determined that human fossils found in Ethiopia in 1967 are 65,000 years older than first thought, from about 195,000 years ago. The revised date, they said, makes the skulls and bones the earliest known remains of modern Homo sapiens.

The research reinforces the theories of an African origin for modern humans, and the earlier date gives the species more time to have evolved the cultural attributes that probably supported its spread to Asia and Europe from Africa. The new date appears to be near the early boundary for modern human emergence, as suggested in recent genetic studies.
Dig it. We've got the earliest distinctly human fossil, and it gives us more information on how the humans evolved. Evolutionary science produced two hypotheses about the early evolution and migrations of humans. New data allow us to distinguish between these hypotheses. Beautiful.

96-102: More on eyes

From Carl Zimmer, Eyes, Part Two: Fleas, Fish, and the Careful Art of Deconstruction. Different populations of cave fish in Mexico lose their eyes the same ways. The different populations each evolved from the same eyed morph, and had the same evolutionary pathway to eyelessness. Why? Because the same gene that causes eyes to develop correctly slows other growth. This would be a poor design for a system, but as an evolutionary hypothesis it gets us testable predictions and a whole host of fascinating new questions about development, ecology and evolution.

Also, fleas have simple eyes, but are descended from an ancestor with sophisticated eyes. Why is there still evidence of stabilizing selection on the function of photosensitive chemicals? Because photosensitivity is useful outside the eyes. In addition to producing evolutionary questions, and using evolutionary hypotheses, it shows how eye functions can be reduced to simpler parts.

Updated 2/17/05 8:42am: Zimmer points out that it's different populations, not different species.

95: Comparing gene expression in different eyes

Thanks to Tsjok45 for the tip.

Comparative Analysis of Gene Expression for Convergent Evolution of Camera Eye Between Octopus and Human -- Ogura et al. 14 (8): 1555 -- Genome Research

Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been known as a typical example of convergent evolution. To study the molecular basis of convergent evolution of camera eyes, we conducted a comparative analysis of gene expression in octopus and human camera eyes.

We found that 1019 out of the 1052 genes had already existed at the common ancestor of bilateria, and 875 genes were conserved between humans and octopuses. It suggests that a larger number of conserved genes and their similar gene expression may be responsible for the convergent evolution of the camera eye.
Evolution produces testable hypotheses about the functioning of the eye. Those hypotheses reveal more data about the evolution of bilaterians.

94: Aligning genetic sequences from different species

ProbCons: Probabilistic consistency-based multiple sequence alignment -- Do et al. 15 (2): 330 -- Genome Research:

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families.
Testable evolutionary hypotheses and methods for studying evolution.

94: Aligning genetic sequences from different species

ProbCons: Probabilistic consistency-based multiple sequence alignment -- Do et al. 15 (2): 330 -- Genome Research:

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families.
Testable evolutionary hypotheses and methods for studying evolution.