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Mouse can do without man's most treasured genes
The mouse is a stalwart stand-in for humans in medical research, thanks to genomes that are 85 percent identical. But identical genes may behave differently in mouse and man, a study by graduate student Ben-Yang Liao and Professor Jianzhi “George” Zhang reveals.
Their results, which have implications for the use of mouse models in studying human disease, appear in the current issue of the journal Proceedings of the National Academy of Sciences (PNAS).
"Everyone assumes that deletion of the same gene in the mouse and in humans produces the same phenotype (an observable trait such as presence or absence of a particular disease). That's the basis of using the mouse to study human disease," said Zhang, an associate professor of ecology and evolutionary biology. "Our results show that may not always be the case."
U-M News Service press release
Image by Ben-Yang Liao
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Illustration by John Megahan, Conus leopardus |
Snail venom study gives insights into biodiversity’s origins
Professor Tom Duda and his former postdoc, Ed Remigio published a study in the February issue of Molecular Ecology on the evolution of venoms of predatory marine snails.
Understanding the role of genetics in the evolution of ecological specialization can provide tremendous insights into the origins of biodiversity and the dynamics of how closely related species adapt to certain ecological niches and appear different from each other (scientists call this adaptive radiation).
However, studying the evolution of genes involved with ecological specialization is difficult because these genes are often not known. Duda and Remigio looked at the evolution of a specialized diet of the predatory marine snail Conus leopardus, a species that preys exclusively on marine acorn worms (hemichordates). The limited diet is associated with a decline in the number and diversity of toxin genes expressed in the venom of this species.
These snails, commonly known as cone snails, use venom to paralyze their prey including fish, other snails and worms. Conus leopardus is the only cone snail known to prey exclusively on acorn worms. To understand how the venom of Conus leopardus has evolved in relation to the origin of its unique diet, the researchers examined the toxin genes that are expressed in the venom of this species. They found that the venom of Conus leopardus is much less complex than venoms of other species. This suggests that dietary shifts and dietary specialization of cone snails is associated with the streamlining of their venoms. |
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Sheep’s surprising role in traditional farming
During the last several centuries, traditional farmers in the high granite mesas in eastern Portugal south of the Douro river invested great effort to tend a large number of sheep. This is in spite of the fact that the sheep produced very few lambs, little milk, low quality wool, and were not eaten. Professor George Estabrook’s research reveals why these farmers invested great effort in caring for so many sheep, reported in the spring/summer Journal of Ethnobiology.
In this major rye growing region of Portugal, about half the rye produced was carried away to feed urban populations. Rye grain was an important nitrogen source for village agro-ecosystem. Farmers replaced this loss using a nitrogen-fixing plant, giesta (Cytisus, Fabaceae), to make compost for crop fertilization. The carbon/nitrogen ratio of giesta is about 30, which is too high for giesta alone to rot readily in the soil.
Farmers kept about 20 sheep for every hectare (close to 2.5 acres) they cultivated. So why keep so many sheep? Farmers mixed their excrement with giesta to lower the carbon/nitrogen ratio to near 15, which enabled it to rot and release nutrients at the rate rye needed them to grow productively.
This paper reports the results from experimental rye plots in the county of Trancoso, Beira Alta Portugal, which demonstrate the importance of mixing sheep excrement with giesta before burying it in rye fields to maintain soil fertility. (Journal of Ethnobiology Volume 28 (1) Spring/Summer 2008) |
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Ants and avalanches: Insects on coffee plants follow widespread natural tendency
Ever since a forward-thinking trio of physicists identified the phenomenon known as self-organized criticality—a mechanism by which complexity arises in nature—scientists have been applying its concepts to everything from economics to avalanches.
Now, researchers at the University of Michigan including Professors John Vandermeer and Ivette Perfecto and their colleagues at the University of Toledo have shown that clusters of ant nests on a coffee farm in Mexico also adhere to the model. Their work, which has implications for controlling coffee pests, appeared in the Jan. 24 issue of the journal Nature. Read the article to see what avalanches have to do with ants.
U-M News Service press release.
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New study uncovers unexpected genetic differences within and between species
A recent study by evolutionary biologist Professor Patricia Wittkopp and colleagues suggests different genetic sources of variation within and between species. This is contrary to most models of evolution in which differences between species are often thought of as an extension of the variation within species. The study focuses on a molecular way in which species vary: how their genes are turned on (or "expressed"). Expression differences can be caused by two different types of genetic changes, and the contribution of the two types was assumed to be similar within and between species.
Surprisingly, the researchers found that this is not the case. Rather, genetic changes that affect expression of only one allele appear to accumulate preferentially over time relative to genetic changes that affect expression of both alleles. (Alleles are different forms of a gene. Humans, fruit flies, and most other animals have two alleles for every gene.) This finding suggests that the types of variation present within a species may not be a good predictor of the types of genetic variation responsible for differences between species.
The paper, “Regulatory changes underlying expression differences within and between Drosophila species” was published in Nature Genetics online February 17, 2008. |
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Gene study supports native American land bridge theory
U-M researchers analyze 678 genetic markers in 29 native populations
Did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?
Professor Noah A. Rosenberg, working with University of Michigan scientists and an international team of geneticists and anthropologists, has produced new genetic evidence that supports the land bridge theory.
The study, published online in PLoS Genetics in November 2007, is one of the most comprehensive analyses so far among efforts to use genetic data to shed light on the topic. (more). See Science News Online and a cool interactive at the American Museum of Natural History (click on Human>Snapshots>Tracing the First Americans).
U-M Health System press release
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First genetic evidence of hybridization in large-bodied New World primates
There are few well-documented cases of natural hybridization among primates. Natural hybridization has only been reported for small-bodied New World species and even among these, no genotypic evidence has ever been presented to confirm the reports. Evolutionary biologists Liliana Cortes-Ortiz, Tom Duda and colleagues present genetic evidence of hybridization of two large-bodied species of neotropical primates (howler monkeys) that diverged some three million years ago.
Their work will likely aid understanding of how new species form, origins of reproductive isolation among primates, and the role of hybridization in primate evolution. “Hybridization in large-bodied New World primates” was published in Genetics, August 2007. |
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Comparing models for early warning systems for neglected tropical diseases
The forecasts provided by early warning systems (EWS) for tropical diseases can be useful in planning services for affected populations. As a result, more accurate estimates can be made for numbers of hospital beds needed, vaccinations, drugs and infection control measures.
Graduate student Luis Fernando Chaves, first author, and Professor Mercedes Pascual, recently published a research paper in PLoS Neglected Tropical Diseases. Using American cutaneous leishmaniasis as an example, their prediction accuracy for the disease burden was as high as 80 percent at time scales of one year or less. Incorporating climate data into their models raised accuracy. At least 2.1 million people are infected with Leishmaniasis annually from Leishmania protozoa, transmitted by sand flies.
Their research outlines three key components for a general approach for the development of EWS. Read the article.
Image Credit: © 2007 Emma Burns
Cover PLoS NTD October 2007 |
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House mouse genes provide clues to reproductive isolation mysteries
In the December 2007 issue of Genome Research, Professor Priscilla Tucker and her colleagues report their preliminary findings based on an analysis of 42 genetic markers in the house mouse species, Mus musculus and Mus domesticus.
They document a nearly 50-fold difference in gene flow across the hybrid zone in central Europe. Multiple genetic markers that show no gene flow likely identify regions of the genome that contain genes contributing to reproductive isolation between Mus musculus and Mus domesticus. Other genetic markers show asymmetrical gene flow, identifying regions of the genome that contain genes with alleles that spread from one species to the other. Their data suggests that the genetic underpinnings of reproductive isolation, even at early stages of divergence, are complex.
Co-authors include EEB graduate student Meg Bakewell, former graduate student Kate Teeter and former biology undergraduate students Janelle O’Brien and Lisa Thibodeau, among others. Read the article.
Drawings: Joe. T. Marshall, “Identification and scientific names of Eurasian house mice and their European allies, subgenus Mus (Rodentia:Muridae). |
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Some marine fishes that bear light organs harboring symbiotic luminous bacteria. Clockwise from the upper left the fishes are: Chlorophthalmus nigromarginatus, Physiculus japonicus, Acropoma japonicum, Caelorinchus hubbsi, and, at the center, Aulotrachichthys prosthemius.
Photographs by A. Fukui.
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Testing coevolution in bioluminescent symbiosis
Professor Paul Dunlap and post-doctoral fellow Jennifer Ast, together with Japanese colleagues, have demonstrated that luminous marine bacteria have not cospeciated with the animals that harbor them in bioluminescent, light-organ symbioses. Their findings, based on an extensive sampling of deep- and shallow-water fishes from east and southeast Asia, contradict the long-held view that bioluminescent symbioses are highly specific, exclusive associations reflecting genetic selection and symbiont-host coevolutionary interactions.
Instead, their work reveals that bioluminescent symbioses are less species specific than previously thought and that in many cases the associations are non-exclusive, with individual host fish harboring two species of luminous bacteria. Furthermore, detailed phylogenetic analyses of these associations demonstrate that the bacteria have not diverged evolutionarily in concert with their host fishes. The implication of their work is that patterns of bioluminescent symbiont-host affiliation observed in nature are likely to arise from a congruence in the environmental distributions of the individual species of bacteria and the animals with which they are symbiotic, not from species-specific genetic selection and coevolution.
Their paper, "Phylogenetic analysis of host-symbiont specificity and codivergence in bioluminescent symbioses" was recently published in the October 2007 journal Cladistics. |
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Unique Cuban hook-billed kites become conservation priority
Research scientist Jeff Johnson, Professor David Mindell, and Russell Thorstrom, a colleague at The Peregrine Fund, have discovered that hook-billed kites from Cuba are genetically distinctive from other hook-billed kites, at levels that merit their consideration as a new, separate species (Chondrohierax wilsoni).
Their Cuban hook-billed kite DNA samples were isolated and sequenced from four museum specimens that were collected in 1895 (112 years old), 1906, 1921 and 1922. This finding adds urgency to field efforts (by collaborators) to determine whether any hook-billed kites survive in Cuba; the last reliable observations of hook-billed kites in Cuba were in 1992.
Johnson is assistant research scientist in EEB and the U-M Museum of Zoology. Mindell is professor in EEB and curator in the UMMZ. Read the paper in Animal Conservation, August 2007. |
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Tracking species movement over time using new modeling techniques
Corinne Richards, EEB graduate student and Bryan Carstens, EEB postdoctoral fellow, published a paper titled “Integrating coalescent and ecological niche modeling in comparative phylogeography” in the journal Evolution, June 2007.
Their research integrates these two types of modeling to look at the genetic structure between four species (a tailed frog, Ascaphus montanus, a salamander Plethodon idahoensis, a vole Microtus richardsoni, and a willow, Salix melanopsis) from the Pacific Northwest of North America. Ecological niche modeling is used to predict where these species would have been found 21,000 years ago during the last Ice Age.
The researchers expected that species ranges had shifted since the Ice Age but they didn’t know where they shifted from except from fossils. The new technique simplifies the tracking of species movement through time without fossils. |
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Tahitian tree snails may still have a future, U-M study suggests
Despite the recent mass extermination of Tahiti's colorful tree snails, it may still be possible to preserve much of their original genetic diversity in the wild, research by Professor Diarmaid Ó Foighil, U-M mollusk expert, and collaborators suggests.
The work, which relied on 600 vials of freeze-dried samples collected in 1970 and left untouched in a U-M freezer for more than 30 years, is reported in the July 3 2007 issue of Current Biology.
Collaborators include Taehwan Lee, Professor emeritus John B. Burch, Younghun Jung, Trevor Coote and Paul Pearce-Kelly.
Feature story: Mountain surprise for threatened snails, Current Biology.
U-M News Service press release
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Organic agriculture can feed the world and help environment
Organic farming can yield up to three times as much food as low-intensive farming on the same amount of land in developing countries.
The study was conducted by a research team headed by Professor Catherine Badgley, Ecology and Evolutionary Biology, and Professor Ivette Perfecto, School of Natural Resources and Environment. The team's results refute the long-standing assumption that organic farming methods cannot produce enough food to feed the global population.
Co-authors and researchers include several current and former U-M graduate and undergraduate students, including Michael Jahi Chappell, EEB Ph.D. candidate.
The study was published in Renewable Agriculture and Food Systems, July 2007, Issue 2.
U-M News Service press release |
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The kapok connection:
Wind and ocean currents explain rainforest similarities across continents
Research by professor and evolutionary ecologist Christopher Dick and coworkers shows that the kapok tree—and perhaps other rainforest trees—actually colonized Africa after the continents split, as a result of seeds traveling across the ocean. The findings were published online June 7, 2007 in the journal Molecular Ecology.
Coauthors on the paper are Eldredge Bermingham of the Smithsonian Tropical Research Institute and Maristerra Lemes and Rogerio Gribel of the Instituto Nacional de Pesquisas da Amazônia. The National Science Foundation, the International Plant Genetics Resource Institute and the Smithsonian Tropical Research Institute provided funding.
Illustration by Zina Deretsky, Science Illustrator, National Science Foundation.
U-M News Service press release |
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