Cincyevolution - Herman's Evolution, Science and Nature Blog

Guangzhou, China

2009-07-17T19:57:00.008-04:00

We are in Guangzhou, China meeting with collaborators at the South China Institute for Endangered Animals. Everyone here has been really kind to us and it looks like there are many areas where we can collaborate together to learn more about the evolution of the birds of East Asia.

Guangzhou is an enormous city of about 12 million people just north of the manufacturing center of Shenzen and the Kowloon Peninsula and Hong Kong (see photo left of the view of Guangzhou from BaiYu Shan Park). We saw perfect habitat for birds along the way but few if any birds. In Taiwan around large cities like Taipei there would be thousands of egrets and other waders in the flooded fields, canals and rivers but here we saw none. The Cantonese apparently have a taste for egret nestlings and probably over centuries have been collecting them from egret rookeries. This continues to this day with legal harvesting at designated colonies. The rules are if a nest has 4 nestlings you can take 2, if it has 3 you can take 2 and if it has 2 you can take 1.

However a few birds remain, but not nearly as many as one would see around Taipei or even Hong Kong. We did manage to see some species including Chinese Bulbuls, Japanese White-eyes, Red-whiskered Bulbul, and Common Tailorbird. Also, we were lucky enough to catch this Collared Scops Owl (Otus bakkamoena) roosting in the bamboo in a park on the campus of Sun Yat Sen University. We venture out into the more rural parts of Guangdong Province this weekend and hopefully add some more species to our trip list!

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Off to China

2009-07-15T10:02:00.006-04:00

I'm sitting in the airport in Chicago waiting to catch a flight to Hong Kong. With generous funding from the Helen B Vogel Trust and the Mary Jane Helms Charitable Trust to Cincinnati Museum Center I'm able to join long-time collaborator Bailey McKay of the University of Minnesota in the field in Southwest China. Together with partners in Taiwan and Mainland China we are hoping to learn about the history of the bird communities of Taiwan. By comparing the birds of Taiwan with their closest cousins in Mainland China using the latest molecular genetic tools we can date the time from which the endemic species on the island of Taiwan split from their sister species in Mainland China. We can match these data to key geologic events in the formation of the island to tell us about the history of the terrestrial ecosystems on the Taiwan.

Bailey is already in China with funding from the National Science Foundation's East Asia and Pacific Summer Institute and has collected many samples from birds in Yunnan Province and I hope to join him to collect more samples, process some samples in the lab and build relationships with our Chinese colleagues. Fa-Sheng Zou of the South China Institute for Endangered Animals in Guangzhou is our key collaborator in Mainland China and an excellent host and intellectual partner in this project. Fa-Sheng's students are also proving to be fantastic collaborators as well.

The photo above is of the White-browed Robin (Luscinia indica) in Taiwan. This is just one of the many species of montane birds in Taiwan whose closest relatives are distributed around Southwestern China. Genetic data gathered from Taiwanese species and their sister species in Taiwan will likely elevate populations of birds on Taiwan to species status and tell us much about the evolutionary history of the terrestrial animals on the island of Taiwan.

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New updates on the cincyevolution website

2009-05-05T21:22:00.004-04:00

A couple new things on the cincyevolution.org website. I've updated the 'lab news' section of the zoology site and finally updated my photo in the 'about the curator' section. Also, we now have a store at http://store.cincyevolution.com where you can purchase books in Cincinnati Museum Center's Science Contributions Series and soon other natural history gifts will be available as well. Enjoy!

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Science and Natural History in the beltway

2009-04-20T21:21:00.010-04:00

I'm back at the museum from last week's trip to Arlington and Washington D.C. where I was able to visit the National Science Foundation and the National Museum of Natural History. The National Museum of Natural History had a nice exhibit called Orchids Through Darwin's Eyes. The exhibit had a fantastic array of cultivated orchids, mostly hybrids but some species as well (like this Brassia orchid from Central America in the photo from the left), and discussed the many adaptations and unique evolutionary history of the orchid family.

The Sant Ocean Hall (see bottom photo) was also fantastic and had some really interesting specimens including a giant squid, a fossil hemiscyllus shark, a Dunkleosteus skull, fossil cetaceans (whales) complete with hind limbs. It was a great exhibit with lots of changes from what I remember as a kid with my first visit to the National Museum of Natural History in the 1970's. The weather was great and the mall and the Smithsonian museums were packed. Museums seem to be as popular as ever and just maybe growing in their popularity.

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Cincinnati Museum Center joins CBOL

2009-03-19T17:09:00.003-04:00

Cincinnati Museum Center is the newest participating member in the Consortium for the Barcode of Life. DNA barcoding involves sequencing a gene common to most of life. These sequences can then be used alongside traditional characteristics as a mark of species identity. Large barcode databases allow for unknown specimens, perhaps from difficult to identify larval or egg stages, to be compared against known sequences permitting species-level identification. Also, DNA barcoding can provide preliminary data that hints at unrecognized evolutionary lineages and thus will prompt more detailed research projects on new species. Cincinnati Museum Center is working with Rockefeller University to identify DNA barcode sequences for Philippine Birds and with the Ohio Biological Survey to build a DNA barcode database for Ohio amphibians. These projects are among the first in the museum's new National Science Foundation funded Molecular Ecology and Systematics Laboratory and the beginning of what hopefully will be a long and productive track record in evolutionary biology.

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DNA lab in the news

2009-03-17T21:22:00.002-04:00

Biostart, a regional life sciences start-up center, did a feature story on Cincinnati Museum Center's new National Science Foundation funded Molecular Ecology and Systematics Laboratory. A video interview on the lab and the role modern molecular genetics plays in modern museum research with yours truly can be found here. Projects on Ohio amphibians, Philippine birds, Great Horned Owls and other organisms are now ongoing. Hopes are that the lab will continue to grow as a regional resource and we'll uncover many exciting finds about life's diversity.

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New blog site

2009-03-10T22:47:00.002-04:00

The cincyevolution.blogspot.com site will still keep readers updated on goings on at Cincinnati Museum Center's zoology department but blogs on the latest research in evolutionary biology have moved to a new site. Monofilia.org is now the new site for my blogs on research in in the world of evolutionary biology. The new site is hosted by Squarespace which provides a powerful and easier to use platform for web/blog management. So, keep on coming back to cincyevolution.blogspot.com for updates on activity in the zoology department at Cincinnati Museum Center and visit monofilia.org for my thoughts on the latest research in evolution.

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Pygmy origins

2009-03-01T20:49:00.017-05:00

Human populations vary genetically, however, much of this variation is not divided into discrete groups but rather is distributed as a cline, or gradually, with one population smoothly transitioning into another. Genetic isolation in most human populations is therefore primarily dictated by distance. Also, the human propensity for roaming and spreading into new environments means that humans spread their genes widely and tend to genetically homogenize populations. However, there are some exceptions to these general patterns. Some human populations have experienced relatively long periods of genetic isolation.

Pygmies of West and Central Africa are known for their comparatively short stature. Pygmies do not comprise a single group but rather approximately two dozen groups with a diverse array of different languages. While on average adult male height is about 5 feet, comparatively small for most human populations, mean height can vary by as much as 8 inches among different pygmy groups. Pygmies are among the last groups in Sub-Saharan Africa to practice the hunter-gatherer lifestyle typical of our earliest human ancestors and as such understanding their evolutionary history can provide important clues to the history and diversification of our species.

Paul Verdu of Paris' Centre National de la Recherche Scientifique and colleagues in the latest issue of the journal Current Biology examined the genetic history of 9 pygmy populations (Bezan, Central Baka, Eastern Baka, Southern Baka, Gabonese Baka, Kola, Koya, Eastern Bongo, and Southern Bongo) and 12 neighboring non-pygmy populations using 28 genetic markers across 604 individuals. As a group, pygmy populations in this study showed large amounts of genetic diversity and, with the exception of the Eastern and Southern Bongo pygmies, pygmy genetic variation clustered together, and separate from non-pygmy genetic variation. Eastern and Southern Bongos showed comparatively more evidence of gene flow with non-pygmy populations, hence their tendancy to cluster within non-pygmy genetic variation.

These genetic data support a common genetic heritage of all West African pygmy populations in the study and an evolutionary split from other West African peoples some 54,000-90,000 years ago. Within the pygmy lineage, divergent populations appear to have arisen more recently, as recent as 2,600-2,900 years ago, the same time agricultural peoples in the region were undergoing expansion. These conclusions are in line with previous results employing other types of genetic markers. Interestingly, Bongo pygmies not only genetically clustered closely to non-pygmy populations but they exhibit the tallest mean height, further evidence of gene flow from non-pygmy populations to Bongo pygmies. Much of this gene flow could be relatively recent and may eventually swamp out the pygmies unique genetic lineage.

The expansion of agricultural peoples in Sub-Saharan Africa likely drove ancestral pygmy populations into increased isolation from one another therefore driving their genetic divergence. Culture and language of indigenous peoples are not the only parts of their history under threat of extinction, but, as human history shows, their very genetic lineage too can be lost to population extinction or genetic exchange among populations. Modern molecular genetics are a powerful tool for uncovering evolutionary history. Being a widespread and adaptable species human populations vary in their genetic history with some being more characterized by isolation and others by mixing. Evolutionary theory provides the critical framework to make sense of rapidly growing genetic data from human populations and shows that humans are subject to the same evolutionary forces that shape the rest of nature.

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Paul Verdu, Frederic Austerlitz, Arnaud Estoup, Renaud Vitalis, Myriam Georges, Sylvain Théry, Alain Froment, Sylvie Le Bomin, Antoine Gessain, Jean-Marie Hombert (2009). Origins and Genetic Diversity of Pygmy Hunter-Gatherers from Western Central Africa Current Biology, 19 (4), 312-318 DOI: 10.1016/j.cub.2008.12.049
Roberta Kwok (2009). Pygmies share a recent common ancestor Nature DOI: 10.1038/news.2009.82

Please stimulate my research!

2009-02-18T23:06:00.002-05:00

The American Recovery and Reinvestment Act, otherwise known as the Economic Stimulus bill, includes 2.5 billion in additional funds for the National Science Foundation (NSF) specifically for "research and related activities". To help build scientific infrastructure 300 million of these funds are reserved for the NSF's Major Research Instrumentation program. An additional 502 million, of which 400 million will go to research equipment and facilities and 100 million to education and human resources, will go to other NSF activities. Incidentally NSF's Major Research Instrumentation program provided funds for Cincinnati Museum Center's (CMC) new Molecular Ecology and Systematics Laboratory. Hopes are this will push the US towards increased innovation in basic science. New proposals to the NSF, if funded, will help CMC grow as a research institution, spread scientific literacy and train students at every level in the high tech skills required for a modern economy. Wish me luck!

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Happy Birthday Chuck!

2009-02-12T22:00:00.004-05:00

Today is the 200th anniversary of Charles Darwin's birth. The notion that life changes over time and the idea that species share a common ancestry both predate Darwin, but, Darwin was the first to provide a viable mechanism by which biological evolution occurs, namely evolution by natural selection. Darwin solidified the idea of evolution and this idea rapidly spread in acceptance among scientists after the publication of Origin of Species.

Evolution's importance can not be overstated. Today evolution is the central organizing principle in the life sciences. To date, it is our only viable explanation for the diversity of life on earth. Data from paleontology, ecology, anatomy and most recently, modern molecular genetics and comparative genomics continue to support the conclusion that life shares a common genetic heritage.

Darwin is a model of how science should work and how scientists should conduct themselves. He was careful, thorough, curious, and dedicated to the details and all the while humble and considerate of his colleagues. Darwin did not have the computational mind of a Newton nor was he capable of the abstraction of an Einstein. Darwin's genius was simply as a clear thinker, ever mindful of the evidence and ready to follow that evidence where it leads. At the center of Darwin's ideas was a broad knowledge of natural history all to be brought to bear on big questions in science.

Darwin and Abraham Lincoln were born on exactly the same day. Both played key roles in building the world we live in today. The bicentenial of their births should be a time to reflect on their accomplishments and follow their example to move society forward.

Happy birthday Chuck!

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Origins blog at Science website

2009-02-03T22:06:00.003-05:00

With 2009 as the 200th anniversary of Darwin's birth and the 150th anniversary the publication of the Origin of Species evolution is spreading across the web faster than a large bill in a drought-ridden finch population. The American Association for the Advancement of Science's Science Magazine has a new blog all about origins. Inspired by Darwin, AAAS will spread news on all things evolution from anthropology to genomics to the origin of life. So check in regularly as part of Darwin year 2009!

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Inauguration day at Cincinnati Museum Center

2009-01-20T19:52:00.006-05:00

Cincinnati Museum Center's Union Terminal opened the rotunda to the community to watch the inauguration of Barack Obama as the 44th President of the United States. Hundreds of people from Cincinnati/Northern Kentucky area were in attendance to watch this milestone in American history. Thanks to the outgoing Bush administration and good luck to the new Obama administration!

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TAIPEI 101 Firework, 2009, Happy New Year

2009-01-04T10:38:00.001-05:00

TAIPEI 101 Firework, 2009, Happy New Year
Originally uploaded by Eric Wang Colorful World

Happy New Years! I found this great photo by Eric Wang on Flickr of the 2009 New Years celebration in Taipei with fireworks blasting off of Taipei 101. Best of New Years wishes to all my readers from Ohio to Taiwan!

Economy hits natural hisory museums

2009-01-02T11:19:00.003-05:00

Chicago's Field Museum of Natural History will cut it's budget by 15%. The Field is not only among the top museums in the country but a center of research excellence in the biological sciences. In an article in Nature News Field Museum associate curator and ornithologist Shannon Hackett worries that severe cuts could jeopardize the museum's stature as a leading research center. Hackett comments, "Once you lose your academic stature, it is very difficult to regain". A major problem lies in loses in the museum's endowment dropping from $320 million in the spring to $215 million in November. Museums around the country are experiencing similar problems. Especially hard hit are those institutions that receive state funding in those states with falling tax revenues. The University of Pennsylvania's Museum of Archaeology and Anthropology has cut 18 research positions and the Virginia Museum of Natural History announced in October that the state has ordered a 10% budget cut resulting in job losses and a reduction in hours the museum is available to the public.

Clearly it is as important now as ever to support your local natural history museum. Visit your museum regularly, consider a membership and if you have the means, donate, so that these vital centers of scientific research and education can continue to grow and thrive. The long term economic health of the US is critically linked to a scientifically literate society where discovery and innovation spawns economic opportunity. Natural history museums are key players in building the scientific literacy required in any successful modern economy.

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Pachyderm Problems for Zoo Elephants

2008-12-16T21:27:00.012-05:00

In the December 12 issue of the journal Science Ros Clubb of the Royal Society for the Protection of Animals and colleagues, including well known elephant researcher Cynthia Moss, report that captive elephants do not live as long as their free-living counterparts, or even as long as working elephants in Burmese timber camps.

Collecting data from over 4,500 elephants from European Zoos, wild populations in Amboseli National Park in Kenya and working elephants in Burmese logging camps, the authors found a significant correlation between captivity and longevity. Females from a well studied population of African Savannah Elephants (Loxodonta africana) in Amboseli National Park in Kenya exhibited a median life span of 56.0 years (these data excluded mortality from humans). African Savannah Elephants in zoos have a median life span of only 16.9 years. As of 2005 when the study ended female African Savannah Elephants in captivity experienced a mortality risk 2.8 times higher than the natural mortality of wild female elephants in Amboseli. Captive-born female African Savannah Elephants die earlier in zoos than in the wild but infant and juvenile mortality was similar between wild and captive elephants.

For Asian Elephants (Elephas maximus) the effect of zoo captivity on mortality was also significant. Captive female Asian Elephants in the study exhibited a median life span of 18.9 years while working Asian Elephants in a Burmese timber operation had a median life span of 41.7 years. While mortality risk in African Savannah Elephants went down over time, suggesting improved captive management, there was no significant reduction in mortality for Asian Elephants. Also, being born in a zoo versus born in the wild had a significant effect on surviorship in Asian Elephants. Ironically, wild-caught Asian Elephants did better in captivity than their captive-born counterparts.

Elephants live in tightly knit social groups of females and juveniles with very long-term associations among individuals. Wild female elephants rarely move between groups, but, zoos regularly transfer individuals among institutions. Female Asian Elephants are moved around among European Zoos approximately once every 7-years. Transfers have an effect on the health of captive elephants. This study found that inter-zoo transfers significantly reduced survivorship in Asian Elephants.

Georgia Mason, a co-author on this study and zoologist at the University of Guelph in Ontario, Canada, discussed the results on the December 12 Science Magazine podcast. According to Mason the situation for American zoo elephants is no better than their European counterparts. 15% of zoo-born elephants in Europe die in their first year while in the USA 40% of zoo-born elephants die before the age of one.

Small group size, frequent inter-zoo transfers, and comparatively tiny enclosures for an animal that has orders magnitude greater home range area in the wild are all likely contributors to the problem of reduced survivorship in zoo elephants. However, solutions to this problem are not straightforward. Large sums of money have been spent in European and US zoos to build larger enclosures for captive elephants but the study by Clubb and colleagues found little evidence that such improvements have resulted in increased survivorship in captive elephants. Some increases in survivorship for African Savannah Elephants have occurred but not nearly enough to bring their surviorship on par with wild counterparts and the study found that despite increased spending and larger enclosures there was no increase in survivorship for Asian Elephants. Mason in the Science Podcast interview pointed out that recent expenditures of approximately 23 million US dollars spent on improving enclosures for the elephants at the Oklahoma City Zoo were greater than the entire annual budget for the Kenya Wildlife Service or the South African National Parks Authority. Perhaps the greatest concern is that captive elephant populations are not self sustaining and can not survive without introduction of individuals taken from the wild.

This study provides a compelling argument for an elevated discussion on not just captive elephants but the welfare of other large-ranging, social mammals as well. Hopefully this study will place a renewed emphasis on future research and novel approaches to captive husbandry of these magnificent mammals.

Clubb, R., Rowcliffe, M., Lee, P., Mar, K. U., Moss, C., Mason, G. J. (2008). Compromised Survivorship in Zoo Elephants Science, 322 (5908) DOI: 10.1126/science.1164298

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Interview with Judge John E. Jones III

2008-12-07T00:24:00.002-05:00

The journal PLoS Genetics has published a wonderful interview with Judge John E. Jones III. A conservative federal judge in the US District Court for the Middle District of Pennsylvania, Judge Jones was recommended for his current position by PA senator Rick Santorum and appointed to the bench by President George W. Bush in 2002. Judge Jones ruled for the plaintiffs in Kitzmiller versus Dover Area School District striking down a school board policy exposing students to intelligent design creationism in the public classroom.

In the PLoS Genetics interview Judge Jones is asked about his own personal views on creationism and evolution. After saying that as a judge he can review a case independent of his personal views he adds,

"I am a person of faith. I'm certainly not an atheist or an agnostic and I see some divine force somewhere. That said, having had a pretty good education, a great liberal arts education at Dickinson College, I must say that I never had any substantial doubts about evolution generally. I had forgotten, admittedly, a lot of what I had learned about evolution back in college. Moreover, a lot had happened since the '70s, so my understanding was rudimentary. But I never had a crisis of confidence about evolution or a reason to doubt that it constituted a valid theory and good science."

Brown University biologist Ken Miller was an expert witness in the trail and recently gave a wonderful lecture on evolution and intelligent design as part of the Cincinnati Museum Center's Dury Science Lecture Series. Here's what Judge Jones had to say about Dr. Miller's testimony in the PLoS Genetics interview,

"I will always remember Ken Miller's testimony in the sense that he did A–Z evolution. And then got into intelligent design. And having laid the foundation with the description of evolution, got into why intelligent design doesn't work as science, to the point where it is predominantly a religious concept."

Contrast this with Judge Jones opinions of the expert witnesses for the defense, particularly Lehigh University professor Michael Behe,

"Another remarkable moment on the science side was Michael Behe, who was the lead witness for the defendants, and a very amiable fellow, as was Ken Miller, but unlike Miller, in my view, Professor Behe did not distinguish himself. He did not hold up well on cross-examination."

That a conservative self-proclaimed "person of faith" appointed to the bench by President Bush rules so desisively against the teaching of intelligent design creationism speaks volumes for the validity of the evolution position and the vacuity of intelligent design from a scientific and, in so much as the idea is applied to public education policy, legal stance.

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Yeast goes with the FLO

2008-12-06T23:04:00.006-05:00

“Share and share alike”, so goes the old adage about equally distributing goods, even at one’s own expense. Darwin’s idea of natural selection explained evolutionary change by posing that traits spread in the population due to the benefits these traits confer on their bearers. Individuals with certain characteristics produce more offspring relative to those individuals with other characters and as a result the population as a whole takes on a different appearance. However, Darwin’s idea couldn’t explain those traits that provide benefits to others at the expense of their bearers. Sharing with others at one’s own expense is called altruism and in biology altruism remained a puzzle for over a century after Darwin.

Then come the 1960’s and William Hamilton. Hamilton said that a rare gene underlying some altruistic behavior could spread despite the cost to the bearer. But how? How could a gene that results in fewer offspring for its bearer spread in the population? Lucky for Hamilton he had an understanding of genetic inheritance that was not available to Darwin. If behavior is directed towards those individuals in the population who also harbor the same genes for altruism then the trait will spread in the population through the recipients of altruistic behavior. Rare genes for altruism would more likely spread if there were a readily observable marker of the same altruistic gene in others. Richard Dawkins popularized this idea in the 1970’s calling it the ‘green beard effect’. In a hypothetical example Dawkins imagined that genes for altruism would result in a marker, such as a green beard, along with the altruistic behavior. With this clear marker of the altruistic gene in others helpers could direct their behavior only towards those that shared the gene for altruism.

Amazingly there is good evidence for the ‘green beard effect’ in nature in several organisms, from slime molds and fire ants. Even more astonishing, there are examples where a single gene is responsible for ‘green beard’ altruism. Scott Smukalla, Marina Caldara, and Nathalie Pochet of Harvard University and their colleagues report in the latest issue of the journal Cell that they have found a ‘green beard’ gene in the budding or brewer’s yeast, Saccharomyces cerevisiae.Yeast is not only the critical component in the making alcoholic beverages but it is also a classic model system in the study of the eukaryotic cell. Yeasts are single celled organisms but wild strains of Saccharomyces cerevisiae in times of stress will aggregate into multicellular mats often called biofilms. These aggregates of cells can protect cells from antibiotics, heat and cold stress, ethanol, and other toxins. The coming together of single yeast cells into a multicellular group is called flocculation and the aggregations are known as flocs. Occurring in wild yeast in response to stress, flocculation allows the population to ride out tough times.

Typical of many organisms grown under the resource-rich and stress-free conditions of the laboratory, times are seldom that tough and many years of culture in the lab have lead to the loss of flocculation in laboratory strains. Comparing a wild, flocculent strain called EM93 with a laboratory strain, S288C, incapable of forming flocs, Smukalla and colleagues found that flocculation fell under the control of a single variable gene called FLO1. This was confirmed by activating the expression of FLO1 in normally non-flocculent S288C cells. Expression of FLO1 resulted in flocculation exactly like that observed in wild yeast. FLO1 expression creates cell membrane proteins that allow cells to recognize and adhere to other yeast cells expressing the FLO1 gene.

FLO1 in Saccharomyces cerevisiae acts like the ‘green beard’ gene predicted by Hamilton as it allows yeast cells to detect others also expressing FLO1 and form multicellular aggregates and thus provide group protection against environmental toxins. But, remember altruism by definition involves a cost to the altruist. Where is the cost? When grown under toxin free conditions and ideal temperatures yeast expressing the FLO1 gene suffer a 4-fold reduction in population growth relative to yeast cultures that do not express the FLO1 gene.

A mixed culture of FLO1 expressing and non-FLO1-expressing cells grown under conditions that lead to flocs results in flocs containing primarily FLO1 expressing cells and free cells that do not express the FLO1 gene. FLO1 is therefore a true ‘green beard’ gene as it promotes the altruistic, social trait (flocculation) and at the same time excludes participation of those cells not expressing the social trait. Requiring FLO1 for cell adhesion eliminates the spread of selfish cheaters, yeast cells that forego the cost of expressing FLO1 while times are good but also reap the benefits of flocs when times are tough.

Research on the evolution of social, altruistic traits like flocculation can shed light on one of the most important transitions in the history of life, the evolution of multicellular organisms from single celled organisms. Saccharomyces cerevisiae, social amoebae, slime molds and many social bacteria move between a single celled and a multicellular lifestyle. Like Saccharomyces cerevisiae, multicellular forms in other microorganisms are often in response to stressful environments. Very early in our own evolution the colonization of harsh environments by our single celled ancestors likely promoted the same altruistic behavior seen in many modern microorganisms today.

S SMUKALLA, M CALDARA, N POCHET, A BEAUVAIS, S GUADAGNINI, C YAN, M VINCES, A JANSEN, M PREVOST, J LATGE (2008). FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast Cell, 135 (4), 726-737 DOI: 10.1016/j.cell.2008.09.037

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Ken Miller speaks at Cincinnati Museum Center

2008-12-02T22:46:00.004-05:00

This Thursday, December 4th at 7:30pm at Cincinnati Museum Center's Union Terminal Dr. Kenneth Miller of Brown University will speak in the museum's Dury Science Lecture Series. Dr. Miller is a cell biologist and author of life sciences textbooks and popular books on the conflicts between evolution and intelligent design creationism.

A vocal proponent of evolutionary biology in the public arena Dr. Miller has been featured on the PBS series Evolution and served as an expert witness in the recent Kitzmiller v. Dover Area School Board case in US District Court of Middle Pennsylvania. Dr. Miller's testimony played a critical role in the Judge John Jones' decision which declared that the Dover school board's policy to promote intelligent design (ID) theory in public school science courses was in violation of the US Constitution's Establishment Clause because, while presented as science, "ID cannot uncouple itself from its creationist, and thus religious, antecedents".

While proving to be highly effective at exposing the deep flaws within this latest version of scientific creationism, ID theory, Dr. Miller has provided a counterpoint to creationist/ID accusations that evolution promotes atheism by being very open about his own personal beliefs in the Christian faith. Miller's highly successful popular book Finding Darwin's God was not only an effective rebuttal against ID but also a personal testimonial of a Christian scientist's ability to reconcile faith with the scientific consensus on biological evolution. His latest book, Evolution and the Battle for America's Soul, dismantles ID arguments and emphasizes the explanatory power of evolutionary biology in making sense of life's diversity.

In a dwindling economy with environmental and energy crises looming larger and innumerable challenges for the US both domestic and abroad the ability to innovate is critical in moving America forward. The launch of the Sputnik satellite in 1957 by the Soviet Union was a wake-up call for the US and spawned an increased focus in science education and research in the 1960's. The rising prominence of China and India in science and engineering is today's Sputnik and Americans need to decide if they want to continue to be leaders and producers of science innovation and technology or followers and consumers of technology provided by other nations.

Far from an esoteric issue the debate between ID creationism and evolution cuts to the heart of science education in the US. On the one side is scientific innovation and adoption of evidence based inquiry and the other is an attempt to roll back two centuries of scientific progress and judge scientific evidence on the basis of narrowly-defined, preconceived socio-religious ideology. Attending Dr. Miller's lecture at the museum center will be an excellent introduction to these critical issues in American scientific literacy and demonstrate that, contrary to what creationists would have us believe, scientific progress need not come at the expense of our religious faith. I hope to see you there.

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DNA lab is coming together

2008-11-04T09:14:00.003-05:00

The new molecular genetics lab at Cincinnati Museum Center is slowly coming together. Supported by a grant from the National Science Foundation this lab will provide the instruments needed to apply molecular genetic tools in research in ecology, evolutionary biology and molecular systematics. The centerpiece of the lab is an automated capillary electrophoresis machine, also known as an automated DNA sequencer, manufactured by Applied Biosystems. We received a new lab bench to support this valuable instrument and provide much needed workspace. We also had to run a new electrical line to supply 220V, 30A power to the sequencer. Researchers from partner institutions such as Xavier University and Thomas More College will be touring the new lab soon and start bringing in students to gain valuable skills in cutting edge molecular genetic tools. The lab is getting some attention in the community as well and a story by staff reporter James Ritchie appears in the Buisness Courier of Cincinnati.

Yesterday I ran the very first polymerase chain reaction EVER at Cincinnati Museum Center. This technique used to copy a specific region of an organism's genome is the backbone of modern molecular genetics. Our first reactions were a test run of some genetic sexing reactions amplifying a seqment of the sex-linked chromo-helicase-DNA-binding gene in Red-shouldered Hawks. This work is done in collaboration with Cheryl Dykstra to learn about growth and development of Red-shouldered Hawk nestlings in Southern Ohio.

I have high hopes for the lab. Keep checking back here and at cincyevolution for more updates on this new line of research going on in molecular ecology and systematics at Cincinnati Museum Center.

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How to collect a blood sample from a bird

2008-09-05T20:50:00.004-04:00

Genetic tools are a major part of modern comparative biology. Museums are the place where much of this sort of research occurs as museums are storehouses of the source material used in comparative genetic studies. Frozen tissue is stored in ultralow freezers or in liquid nitrogen for a variety of organisms comprise genetic resource collections or GRCs. Ideally tissue samples should be associated with a voucher specimen such as skeletal material, a stuffed skin or a pickled specimen. This allows researchers to check the identity of the tissue sample or compare genetic data with morphological data derived from the source specimen. In ornithology there is a growing trend to collect a blood or feather sample from a bird and release the bird back into the wild. A digital photo together with carefully taken morphological measurements can serve as the voucher for the blood sample. While this is not the "gold standard" way to build a bird collection it can augment traditional collecting efforts and increase numbers of samples while minimizing the effect of collecting on avian populations. Below is a video of me collecting a blood sample from a House Sparrow (Passer domesticus) caught just outside the Geier Collections and Research Center at Cincinnati Museum Center. When done properly there is no evidence of adverse effects on the bird, even though surely it is not an experience they enjoy!

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New National Science Foundation funded DNA lab at CMC!

2008-09-04T20:20:00.004-04:00

Fantasic news for zoology research and education at the Cincinnati Museum Center. We just received an award from the National Science Foundation to fund the purchase of instruments for a molecular ecology and systematics laboratory in the zoology department here at the Cincinnati Museum Center! The centerpiece of this new laboratory will be an automated capillary electrophoresis machine. This piece of equipment will allow for DNA sequencing and multilocus genotyping to be done completely in house at Cincinnati Museum Center's zoology department. Numerous projects are already planned to be conducted in the new lab covering a diverse array of topics, everything from DNA barcoding of Neotropical land snails to the population genetics of owls to amphibian conservation genetics to characterizing the genetic mating system of songbirds. The new lab will have close partners in the region including the Cincinnati Zoo, Thomas More College, Cincinnati Country Day School and Xavier University and will facilitate research, future funding opportunites and educational experiences in cutting edge life sciences techniques for high school students and educators, undergraduates, graduate students, local college and university faculty and our dedicated volunteer staff.

Now I just need to think of a name for the lab! I was thinking of the CincyMolES Lab (Cincinnati Museum Center Molecular Ecology and Systematics Laboratory). We could have a Star-nosed Mole as our mascot maybe? OK, I don't study mammals but it's a neat critter and I thought the name was catchy! I'm happy to field other suggestions from my readers.

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AOU/COS/SCO 2008 Meeting in Portland: Part II

2008-08-12T13:59:00.006-04:00

Last week was the joint conference of the American Ornithologist's Union, the Cooper Ornithological Society and the Society of Canadian Ornithologists in Portland, Oregon. There were many excellent presentations on a variety of topics in ornithology. Below are, in my opinion, some of the highlights from the conference representing the cutting edge of avian research in North America.

- Rosemary Grant of Princeton University presented a plenary lecture summarizing her collaborative work with her husband, Peter Grant, and numerous students and post-docs on the evolutionary biology and ecology of Darwin's Finches in the Galapagos Islands. The Grants' work on selection on bill size in Darwin's Finches is a classic work, arguably the most famous and well supported examples of Darwinian natural selection in the wild. Now the Grants are tackling speciation and presenting their ideas on how Darwin's Finch species arise over time. Whether or not many currently recognized species of Darwin's Finch are indeed true evolutionary species or complex, polymorphic populations was a hot topic of debate behind the scenes in the lobbies of the Hilton and the bars and restaurants on the streets of Portland. It remains to be seen how the Grants' ideas on speciation will stand up to the scrutiny of their ornithological peers.

- Terry Chesser of the National Museum of Natural History along with co-authors from museums around the country such as the University of Kansas and Louisiana State University presented new data on the relationships of one of the largest and most problematic groups of passerine birds, the Neotropical ovenbirds of the family Furnariidae. The woodcreepers were found to be monophyletic (meaning all the birds currently assigned to the woodcreeper group were found to share a single common ancestor). Two main groups were distinguished within the Furnariidae the woodcreepers and the "true" furnariids, or simply the rest of the furnariids.

- Townsend Peterson of the University of Kansas discussed the power of museums in understanding the spread of animal-borne diseases (aka zoonotic diseases). The "bird-flu" or H5N1 virus has the potential for a global pandemic and since 2003 has persisted as a lingering threat to human health, especially in south and south-east Asia. Peterson's group found in surveys of birds collected from south China that H5N1 is not exclusively a disease found in galliform birds (chickens, etc.) and waterfowl but is also found among passerines (i.e. songbirds) and other wild landbirds. Peterson also used bird banding databases to model the potential outbreak of zoonotic, bird-borne diseases, like H5N1, in North America and found that where the outbreak starts can have dramatics effects on the spread and geography of the subsequent spread. All of these findings can only be possible with large museum-led databases of both specimens and large scale sighting and banding records.

- John Wieczorek of the University of California at Berkeley presented an update on the ORNIS database. ORNIS is a distributed database that links together avian data from dozens of museum collections. Today the ORNIS database allows one not only to access holdings on avian specimens but also millions of sighting and banding records, digital photos and sound recordings. Wieczorek also discussed a new online tool, BioGeomancer, to add georeferencing data to existing specimen, photo, recording and sighting records. The power of these online, distributed databases and the georeferencing tools that accompany them was seen in numerous talks during this meeting. With adoption of it's new KE EMu database Cincinnati Museum Center is poised to join these other institutions in making it's collection more accessible and usable by researchers in novel and powerful ways.

- An entire session was devoted to the hot topic of subspecies in ornithology. The traditional way in which scientists name species is the binomial, the familiar genus and species names given to every organism. However, there is variation within species and to incorporate this variation into taxonomy many have adopted a trinomial system of nomenclature consisting of three names for each species, genus, species and subspecies. Kevin Winker of the University of Alaska at Fairbanks gave a good history of the use of trinomial nomclature in ornithology and discussed why divergence in phenotpyes (those characteristics of an organisms most often accessible to direct observation such as size, color, etc.) is not also equal to genetic divergence. This means that often the readily observable, physical traits used to distinguish between different subspecies of birds may not correspond to much genetic variation and thus may be of little evolutionary significance when it comes to distinguishing independent genetic lineages. Susan Haig of the USGS Forest and Rangeland Ecosystem Science Center discussed the problems that differing species concepts and subspecies designations pose for conservation efforts. Haig believes that subspecies designations are critical for conservation and law enforcement purposes even if their biological footing is less than solid. These points were hotly debated in the session and in discussions outside the talks.

- Perhaps my favorite talk of the entire conference was by Matt Carling and Rob Brumfield of the Louisiana State University Museum of Natural History. An idea in evolutionary biology known as Haldane's Rule says that in hybrids the sex that contains two different sex chromosomes (the heterogametic sex) should be less fit than the sex that contains two of the same sex chromosomes (the homogametic sex). A bad version of a gene can be overruled by the action of a good version of the same gene on another chromosome. Therefore heterogametic hybrids will be affected by all deleterious alleles on a sex chromosome. Haldane's Rule has been shown to predict the weaker sex in hybrids in everything from insects to mammals. In humans, and most other mammals, males are the heterogametic sex by virtue of having X and Y sex chromosomes while females are the homogametic sex having two X chromosomes. However, in birds females are the heterogametic sex with W and Z chromosomes and males with two Z chromosomes. Lazuli and Indigo Buntings hybridize in the central US. Carling and Brumfield measured the change in gene frequency across a hybrid zone between Lazuli and Indigo Buntings for both nuclear genes and genes linked to the sex chromosomes. They found much smaller genetic clines for sex-linked loci than for autosomal loci (those loci on chromosomes other than sex chromosomes). This is consistent with sex linked genetic incompatibilities in the hybrids. They also identified one locus in particular that contributed very heavily to this narrow genetic cline in Lazuli and Indigo Buntings. This loci was matched to a similar sequence in the chicken genome which, in chickens, contributes to the failure to lay eggs. Essentially Carling and Brumfield have identified an important gene which contributes to the maintenance of Lazuli and Indigo Buntings as discrete species. An amazing study which I hope to hear more about in the future.

- A fantastic symposium was presented on the last day of the conference in which some of the top curators and collections managers in ornithology presented techniques on preparing and managing material in avian collections. University of Kansas curator Mark Robbins and University of Washington Professor Emeritus Sievert Rohwer presented a live demonstration of their study skin preparation techniques. With some relatively minor differences our volunteers in the ornithology collection at Cincinnati Museum Center are preparing specimens like the pros do it, however, I did pick up some useful tips that will improve our specimens. Kimberly Bostwick of the Cornell University Museum of Vertebrates demonstrated her techniques for preparing skeletal material from bird specimens, again as a live demonstration. This was also very useful as here at Cincinnati Museum Center we plan on a major push towards increasing the collection's avian skeletal holdings. Also, Kevin Winker of the University of Alaska at Fairbanks presented a general overview of the tools of the trade for avian collecting from the intricacies of the permitting process to auxillary barrels for a shotgun! All of the talks in this session provided useful tips for the growing bird collection at Cincinnati Museum Center but they also reaffirmed that the changes implemented in our protocols have put us on the right track towards having a world class ornithology collection.

-Finally Irby Lovette of Cornell University presented some interesting, if not troubling, results on measuring genetic diversity using molecular genetic markers. Researchers for various reasons often want to know the genetic diversity of an individual organism. Genetic diversity in an individual is typically measured in terms of heterozygosity. At any particular location in an individual's genome (at least for sexually reproducing organisms) there will be two copies of a particular gene. If those two copies are the same the individual is homozygous at that locus if they differ then the individual is heterozygous a that locus. Researchers use different types of genetic markers to determine the degree to which an individual is heterozygous across it's entire genome. However, Lovette demonstrated that different markers do not agree with one another on genome-wide heterozygosity. A level of heterozygosity determined using one type of marker may not correspond to the same level determined by another marker. Even multiple loci of the same types of markers often do not agree. This work is consistent with previous findings showing that levels of relatedness and inbreeding were only evident using very large numbers of genetic loci and that molecular genetic markers were inferior to good pedigree data in determining genetic diversity. However, there are many correlations in birds between molecular genetic based genetic diversity and various fitness measures, such as hatching success or growth or behavioral measures. The question then is what do these correlations mean? This will be a fertile field for future research for sure!

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Two other CMC blogs of note...

2008-08-10T16:54:00.002-04:00

OK, I'm sitting in the airport in Denver on my way home and was getting caught up on blogs from my Cincinnati Museum Center colleagues. I encourage everyone to check out Dr. Glenn Storrs' blog for his annual dinosaur field school in Montana at cincymuseum.blogspot.com and Jason Dennison's museum professionals blog at youngmuseumprofessionals.blogspot.com. Enjoy!

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AOU/COS/SCO 2008 Meeting in Portland: Part I

2008-08-10T12:10:00.008-04:00

This week was the joint conference of the American Ornithologist's Union, the Cooper Ornithological Society and the Society of Canadian Ornithologists in Portland, Oregon. This meeting celebrated the 125th anniversary of the American Ornithologist's Union(AOU) and ushered in a new president for the AOU, Dr. Edward "Jed" Burt who is a faculty just down the road from Cincinnati in Delaware, OH at Ohio Wesleyan University. It was a great meeting and many important ties were forged between Cincinnati Museum Center and researchers and natural history museums around North America and the world. I meet with friends and colleagues from the University of Windsor, University of Alaska at Fairbanks, the Taiwan Endemic Species Research Institute, University of Cincinnati, Auburn University, the Delaware Museum of Natural History, the Cleveland Museum of Natural History, and many other colleges, universities and museums and promoted greater use of the collection and plotted out new collaborations and research projects.

There were many excellent talks on the latest findings in ornithology and my next blog will provide a survey of some of the highlights, but, perhaps most useful was a nearly day long symposium on avian museum collections that included live demonstrations of the latest preparatory methods from some of the top curators and collections managers in the country. This symposium in particular proved to be invaluable and provided me with a wealth of information from preparation to permits that will greatly improve the collection at Cincinnati Museum Center. Also, meeting with colleagues and forging new ties resulted in several new projects. The plan is have in house research at Cincinnati Museum Center result in at least 10 new publications over the next year. A bold goal but one that can be achieved through the numerous collaborative efforts between Cincinnati Museum Center Zoology Department and top researchers in avian biology from around the globe.

Of course I take every opportunity to increase the collection at Cincinnati Museum Center and collected many digital photos to go into a growing georeferenced digital resources database for birds. The meeting reinfornced the utility of this growing type of natural history collection in several talks regarding the ORNIS distributed database system. I gained new insight during this part of the meeting on how to manage these collection and provide proper georeferencing (location data critical to making a useful digital resources collection). Also I learned of new ways in which digital resources in ornithological collections are being used alongside both traditional material (skins, skeletons, spread wings, etc.) and frozen tissue collections. Shown in this blog entry are three new digital photos to be archived in a growing digital resources database for ornithology (Top, Northern Fulmar; middle, Barred Owl; bottom, Pacific-slope Flycatcher).

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On the flip side...

2008-07-15T08:43:00.007-04:00

Critics of evolution often point to a perceived lack of transitional forms in the fossil record as evidence that some forms of life don't share a common genetic heritage but rather arose independently. Creationists have been using this line of argument for over a hundred years. But, they do so in spite of the evidence. Intermediate forms are those organisms that have a mosaic of characteristics linking two seemingly unrelated groups or an organism that exhibits a character state in between those found in two or more other organisms. Creationists claim these forms are lacking in the fossil record. However, the transition between theropod dinosaurs and modern birds, the evolution of the mammalian ear bones from a reptilian jaw, the evolution of whales from terrestrial mammals and even the fossil record for our own species are all classic examples of evolutionary transitions complete with several intermediate forms.

Add to the growing list of evolutionary transitions another example from the fossil record. Vertebrate animals have a bilateral body plan, that is they exhibit a front and back and dividing the body down the middle results in two symmetrical sides. There are few exceptions to the symmetrical vertebrate body plan. One striking exception familiar to us all are the flatfishes (Order: Pleuronectiformes). This group includes fish found at your local market or seafood restaurant including sole and halibut. Adult flatfishes are asymmetrical. They start off life with the typical symmetrical body found in other fishes however as they grow their skull undergoes a radical developmental change with the eyes rotating to one side of their head. A flatfish on the sea bed is therefore a fish essentially lying on it's side with an asymmetrical head. Imagine lying on your left side with both your eyes on the right half of your face and you'll get the picture.

The question is how did this unusual body plan evolve? There are clear benefits to exploiting an open ecological niche and becoming specialized to be a bottom feeder but doing so can mean a radical change in an organism's body plan. The flatfish body plan clearly evolved from a typical symmetrical fish plan. Comparing the details of flatfish anatomy and their genes shows that they fit within the large radiation of bony fishes, nearly all of which have a symmetrical body plan. Also, the turbots (Psettodes sp.) are the living representatives of the earliest branch of the flatfish family tree and it, as expected if flatfish evolved from a symmetrical ancestor, they have one eye that doesn't quite make it all the way around the head during development. What's more, the adult asymmetrical flatfish plan develops from a symmetrical larval body plan. Together all these data indicate that the asymmetrical flatfish plan evolved from a symmetrical ancestral body plan. However, as creationists are fond to ask, where are the intermediates?

Along comes University of Chicago evolutionary biologist Matt Friedman. In the July 10th edition of the journal Nature Friedman provides evidence for the evolutionary transition between symmetrical bony fishes and the asymmetrical flatfishes. Friedman provides highly detailed descriptions of fossil fishes in the genus Amphistium and describes a new species, Heteronectes chaneti. These fossils were available to researchers before, however, Friedman applied computed tomography to the specimens to obtain detailed three-dimensional images of their anatomy. Computed tomography involves moving an x-ray source and detector around a specimen and digitally reconstructing a detailed three-dimensional image from the x-ray exposures. Previously it was difficult to tell an asymmetrical flatfish-style skull from a symmetrical skull crushed by the weight of sediment during fossilization. With the new imaging technology Freidman concluded that these fossil fish do indeed show different intermediate stages leading to the fully asymmetrical modern flatfish body plan. Specifically, the part of the skull containing the orbits, the neurocrania, rotates over evolutionary time. A close relative of the flatfishes, Trachinotus, shows the classic symmetrical condition with one eye on either side of the head. The fossil Amphistium and Heteronectes show an intermediate stage with one eye squarely on one side of the head and the other eye on the other side of the head but shifted up towards the top of the head. The earliest branch on the flatfish family tree, the turbots, one eye rests nearly on top of the head and in the rest of the flatfish the eye has migrated fully to the other side of the head.

New findings are popping up all the time from fields ranging from paleontology to developmental genetics that affirm the conclusion that life shares a common ancestry and that these unusual body plans, such as the asymmetrical head of a flatfish, have arisen through evolutionary processes.

Friedman, M. (2008). The evolutionary origin of flatfish asymmetry. Nature, 454(7201), 209-212. DOI: 10.1038/nature07108

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