Darwin's Bulldogs: 2008

Monday, December 22, 2008

Phylogenomics suggest ratites lost flight multiple times

Rebekah Wukits discusses recent findings about ratite evolution for Bio 135.

Ratite evolution has been debated for centuries. Some of the earliest evolutionary biologists questioned whether or not ratites had a linear evolution or if the major groups had had independent origins. Richard Owen proposed that living ratites had much more in common with other flight capable groups while being united by the “arrested development of wings unfitting them for flight”. In 1951, two ornithologists, Mayr and Amadon, stated that, “the present consensus is that the main groups of these birds are of independent origins”.

Traditionally, ratites have been considered to be monophyletic, or ascending from a common ancestor. They are placed in the major group Noegnathae, with the flight-capable tinamous as a sister group. Since the extinct tinamous were capable of flight, it has been thought that the ratites lost flight once in their history, then diversified. Unfortunately, simple geography contradicted this theory. All living ratites (rheas, cassowaries, emus, ostriches and kiwis) are isolated on different southern continents. Rheas are found in South America. Ostriches reside in Africa. Emus and cassowaries are found only in Australia and kiwis can be found in New Zealand. Extinct species of ratites follow the same pattern. Moas were also found in New Zealand, and elephant birds lived in Madagascar. The question became that if flight was lost once early in ratite evolution, how did they become so spread out and isolated? The perfect answer seemed to reside in the theory of continental drift. Ratites came from a single ancestor, lost flight and were then isolated when Gondwana broke up.

Though most of the recent studies of morphological and molecular ratite characteristics have supported the monophyletic theory, many still debate it. Rarely challenged is the fact that adaptations to a cursorial lifestyle, one that is adapted to running, can lead to convergent evolution, and can be misleading when basing phylogeny on morphology. This led scientists to do further phylogenomic studies in order to test the prevailing theories. These studies include data taken from genetic loci that represent the entire avian genome. In this particular study, data was taken from 20 loci that are dispersed widely throughout the avian genome. The data set included all living ratites and eight outgroup taxa. Previously done similar genetic tests have supported ratite monophyly, however these tests were more sophisticated and advanced and supported a different conclusion.

The results are as follows: analysis of the data strongly supports placing the flight capable tinamous within ratites and ostriches as the sister group. If this new phylogeny is correct, the single loss of flight in ratites is unlikely. In order for all ratites to have lost flight in a common ancestor, the tinamous would have had to regain flight at a later time. It is much more likely that flight was lost multiple times do to convergent evolution than to have gained flight in the earliest ancestors, lost flight in the common ancestor of ratites, than gain flight again in tinamous.

It seems more likely that ratites descended from a single ancestor, than diversified when gondwana broke up. Flight was lost in each family and convergent evolution occurred due to similar environmental conditions. Flight is very costly both energetically and morphologically. Ratites had little pressure to fly and since these features are costly to maintain, they became reduced over time. The theories of this paper seem concrete however more study is needed. Their own genetic studies produced conflicting results. Placing tinamous within ratites has great implications for their evolution and dispersal. This idea needs to be further developed and supported.

Reference:

J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds Proceedings of the National Academy of Sciences, 105 (36), 13462-13467 DOI: 10.1073/pnas.0803242105

Wednesday, December 10, 2008

Studying the Flamenco Dance of the Jumping Spider

If you were intrigued by the video you saw in class of the mating dance of jumping spiders, this will show you a bit more about how one can go about studying such fascinating complex behaviors.

Why Sex?

Apropos of the recent steamy discussions in class about sex and evolution, Sonica Sangha shares this video she found on the PBS website:

[via Evolution: Library: Why Sex?]

And as a bonus, here's a behind-the-scenes video podcast accompanying the wonderful PBS Nature series "What Females Want and Males Will Do" which aired last spring. Click on the show titles for more fun video clips and information from the PBS Nature website.

Wednesday, December 3, 2008

Modeling the emergence of multi-drug resistant TB hot zones

Rebecca Freeman submitted this essay for the Evolution class.

According to the World Health Organization (WHO), a “hot zone” is an area with >5% prevalence (or incidence) of Multi-Drug Resistant Tuberculosis (MDRtb). Sally M Blower and Tom Chou have been using a mathematical method to track the emergence and evolution of multiple strains of drug resistant tuberculosis, but they have now developed a new, more complex mathematical model. Before this model, there was only a two strain model, meaning it was only relevant to individuals that can be infected with a wild type pansensitive strain or a drug resistant strain, but there are many more strains then this. There are a resistant strains only to one drug and some resistant to multiple drugs. This means there is a multitude of strains in these hot zones and there was a need for a better way to track this (Blower and Chou 2004). Blower and Chou realized that a more complex mathematical model is necessary to capture the complexity of the epidemiology of the hot zones, and the evolution of hot zones was very unclear

Understanding drug resistance is important to understanding the, and Blower and Chou explain the evolving of resistance very well. They give three processes that are involved in generating drug resistance: Transmission of drug resistant strains to uninfected individuals, which is transmitted resistance; Conversion of wild pansensitive cases to drug resistant cases, which is acquired resistance; finally, cases where they have drug resistant strains and it becomes resistant to more antibiotics during treatment, which is amplified resistance. What everyone has had to do in the past is just study acquired and transmitted resistance, and now with the new model, they can incorporate amplification resistance. This was a big problem because it has been shown that inadequate treatment of DRtb can result in the amplification of drug resistant strains, which may be an important process of MDR epidemics (Blower and Chou 2004). So this is where Blower and Chou came in. They created a model, the call the amplifier model, that enables the tracking of emergence and evolution of MDR strains, the transmission of these strains and the amplification of these strains during repeated episodes of treatment.

Blower and Chou are really studying the effects of inadequate treatment programs, and how this may lead to a higher prevalence in MDRtb. One problem that this research cannot completely take into account yet is the transmittance ability of MDRtb compared to pansensitive tuberculosis. This is an area that is hazy right now, and so this cannot completely be incorporated into the model. Amazingly, they have measured a general fitness of MDRtb vs. pansensitive tuberculosis, by calculating the treatment fail rates and treatment cure rates of the each category of strains.

The authors were very clear with the purpose of the model. Even though the mathematical model is very complex, the idea and how they explain it is easily understandable. They use R0 to stand for the average number of secondary cases caused by one infectious case in a population where treatments are available. Their model breaks this up into four categories of strains: The wild type pansensitive [R0(1)], which is sensitive to all drugs; Pre-MDR [R0(2)], which is sensitive to one of the main drugs used to treat tuberculosis; MDR [R0(3)], which is resistant to both of the main treatment drugs; and post-MDR [R0(4)], which is resistant to both of the main antibiotics and others as well (Blower and Chou 2004). With the information gathered from over 30 years of date they constructed likely evolutionary trajectories of hot zones, and with this they also took into account low cure rates vs. high amplification probabilities in many areas. They also tried to incorporate which strains are more transmissible, but as I said before this was not really possible with their model and there was a large degree of uncertainty.

The results of their model matched the WHO predictions well, but there were some distinct differences, and I think these differences are what make this research so important. By using all for types (R01-4) they found great variability in incidence and prevalence. When treatments were originally started strains of pre-MDR strains emerged quickly, so incidence and prevalence of pre-MDR strains increased, and this subsequently led to possible amplification of resistance and MDRtb epidemics in certain areas. The question is: Why certain areas and not others? This question is explained by Blower and Chou. Interestingly, areas with bad treatment programs do not necessarily have a really high incidence of MDRtb, it has stayed pretty steady at a 5%-14% (Blower and Chou 2004). This to me seems like an argument that MDRtb is not as easily transmissible, because its rates overall have stayed pretty low, but there was no significant evidence for this. The WHO predictions state that a >5% prevalence OR incidence in MDRtb equals a hot zone. Blower and Chou found the mathematical relationship between MDR prevalence and incidence. MDR prevalence can be three times greater then MDR incidence. They used the results to evaluate the hot zones on prevalence or incidence. If it is by incidence then only 20% of those areas would be considered hot zones and 51% if criterion is prevalence (Blower and Chou 2004). I see this as an argument for the fitness of MDRtb to be very high and transmissible ability to be lower, because there are less new cases, and more cases that have just become more resistant.

When looking at the four strains the hot zones had a much lower R0 for pansensitive strains (median=.82), which suggests that the wild type strain should be slowly eradicated. The R0 for the pansensitive strains in non-hot zones were all above 1 (median=1.39) Looking at the rate of detection of cases and treatment rates in hot zones versus non-hot zones it is 55% to 25% (Blower and Chou 2004). This shows that places where they have control programs were successful at fighting pansensitive strains but ironically it created more MDRtb strains, making it more likely to become a hot zone.

The importance of this research is that they have figured out that the difference between incidence and prevalence rates is significant enough to change the view of an area as being a hot zone or not. Their research looks at many factors that go into the evolution of these hot zones. Out of the many factors they actually saw that case detection and treatment rates were the most important factors. They came to this conclusion because if case detection and treatment rates were low, and the amplification was high, it still did not generate a hot zone. Vise versa, if the case detection and treatment rates were high and the amplification rates were low; it was likely to become a hot zone. The point is that these areas with high case detection and treatment rates should not increase these rates unless high cure rates are achieved first. Blower and Chou have created a model that has multiple dimensions and can help the WHO in the future to prevent hot zones from popping up in high risk regions. The WHO already had a model for this but it was nowhere complex enough to correctly calculate prevalence and incidence of MDRtb, and how their mathematical relationship.

Reference:

Sally M Blower, Tom Chou (2004). Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance Nature Medicine, 10 (10), 1111-1116 DOI: 10.1038/nm1102

On Hormonal and environmental control of neuroplasticity

Andrew Mora review's Christy Strand's seminar on neuroplasticity.

Nueroplasticity is an interesting concept that deals with changes in the brain due to experiences. In order to study neuroplasticity better, Dr. Christy Strand used hormonal and environmental cues to see how they would affect the brain. The specific region of the brain that Strand was interested in was called HVC (high vocal center in birds) and the size of this region of the brain was recorded before and after experiments. According to Strand, this region in birds is important in motoring song output, and is also involved in song learning. She asserted that testosterone, an important steroid that affects the brain, did in fact increase HVC volume, but was uncertain as to how the region got bigger. Did individual neurons get bigger? Was the density decreased? Or were there simply more neurons from new cells?

In order to test for the size of the HVC, Strand used bromodeoxyuridine (BrdU) which is a cell birth marker. She used house finches because they are very common throughout the US and they are great song birds to test for the HVC region. Besides using testosterone treatment for the birds, she also wanted to know the role of the photoperiod in increasing HVC growth. Her results indicated that testosterone treatment does affect HVC growth, that photoperiod alone might affect HVC growth, and that testosterone treatment does not affect the number of new HVC neurons, despite an increase in total neuron number. Her reasoning for this might be because of a natural turnover; that is, there is no new neurons being created, but there is a decrease in cell death. Corticosterone (a stress hormone) had no affect on HVC growth.

In another related experiment, Strand used rufus-winged sparrows to test environmental cues on HVC. She used these birds because they have a unique characteristic of beginning their breeding season after the first monsoon in southern Arizona and northern Mexico. Breeding season is important for HVC size because the birds are singing frequently when they are looking for a mate. According to strand, the testes of these birds are big in March, but only used in July when the first rain falls. Her results found that during breeding of these sparrows, HVC neuron number does not increase, and testosterone levels were not different on sampling dates. She did find that singing behavior increases during the breeding season, but was still unsure whether or not HVC affects singing behavior or if the reverse was true.

I particularly enjoyed the area of future research being done by Dr. Strand. She discussed that she will be experimenting with hormonal factors affecting neurogenesis and neuroplasticity in adult snakes and lizards. She will look at the affects of captivity on neurogenesis and affects of sex on neurogenesis. Instead of the HVC region she will look at the size of the medial cortex in adult rattlesnakes. I like this integration because it attempts to compare research done on birds with similar research done on reptiles. Hopefully we will see this work published soon.

The role mtDNA plays in the evolutionary differentiation of species

Bob Koons shares his reflections on a Biogeography class discussion from some weeks ago. I've been unable to upload many student submissions to this blog due to severe tendonitis which limited my computer use for some time, but I'm beginning to catch up and hope to have the remaining student submissions uploaded before the semester ends!

Neotropical diversification of montane populations have been studied mainly in the lowlands of geographical regions simply due to the fact that there is a much larger diversity of species inhabiting the lowlands compared to the highlands. Studies use multiple approaches of statistical methods to get their data to agree. Which test is the best one depends upon the question being asked?

Species can be traced back to their origins using mtDNA, which is directly passed down from the mother. A species that has genetic ties to an ancestor and all its descendant taxa is called monophyletic and a species that has an ancestral taxon and some, but not all, of its descendant taxa; an artificial taxon. (Lomolino et al 2006) Geography plays a role in how a species diversifies over time as was demonstrated by the Finch scenario. The finches migrated south from Mexico to the Northern Andes Mountains of South America. Some finches traversed the Andes and migrated south along the east side of the Andes. The geographic isolation separating the two groups allows for natural selection to run its course allowing for the distinct differences we see in the finches today.

So does this apply to humans also? Can human mtDNA show this geographical divergence differentiating our species? An article entitled, “Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison” by John Huelsenbeck and Nikita Imennov compare the two main theories of the origin of the humans, which are the “out of Africa” and the “regional continuity hypothesis. The “out of Africa” hypothesis relates that modern humans all came from a common ancestor in Africa. Humans spread from there to all parts of the globe, and subsequently wiping out other “homos” that were encountered. The “regional continuity hypothesis” says a single species of homo originated throughout the old world connected through gene flow, after any migration from Africa occurred. Statistics using mtDNA show that the out of Africa scenario is the most possible origin for modern humans. A Bayesian inference statistical analysis was used to accommodate phylogenetic uncertainty from all trees then comparing the probabilities. Bayesian statistics is defined as, “Of or pertaining to statistical methods that regard parameters of a population as random variables having known probability distributions.”In their article Huelsenbeck and Imennov 2002 state, “In this study, we point out how Bayesian inference can be used to accommodate phylogenetic uncertainty when comparing five different models for the origin of modern human mtDNA.” 200 sequences of mtDNA were analyzed, each sequence was 428 sites long, from the hypervariable region I (HVRI) of the mitochondrial region of modern humans and an out group sequence from Neanderthal mtDNA. They used 40 sequences from each geographical region of the globe in their analysis; Africa, Europe, Asia, Americas, and Australia were represented. As discussed in class, and in this paper, a statistical analysis can be modified in many ways. This study used a uniform prior on all possible trees, another way to analyze the data would be to perform a coalescence prior, or to chose another method reconstructing the ancestral geographic area of human mtDNA. Another way of statistical modifications could include a stochastic two-stage model or a coalescence process with different populations connected by variable levels of migration. Still other ways exist that can modify an analysis; the trees could be reconstructed using a molecular clock restraint and incorporated into a Bayesian or maximum likelihood framework. (Huelsenbeck and Imennov 2002) A DNA sequence from Neanderthals may give a clearer answer to the out of Africa hypothesis. MtDNA can be useful to determine human geographic origin after all. Whew! From this we can clearly see that data can and is modified in many different ways to suit a desired outcome.

References:

Huelsenbeck, J. and Imennov, N., 2002. Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison. In Systematic Biology Vol. 51, No 1 pp.155-165.
Lomolino, M.V et al. 2006. Biogeography. MA: Sinauer Associates.
Dictionary.com, Bayesian Statistics. Retrieved October 5,2008.

Monday, December 1, 2008

On the Origin of Species - revisited via the ghost of Asa Gray

As you are probably aware, especially if you are a student in my Evolution class, Charles' Darwin's seminal work "On the Origin of Species by Means of Natural Selection" has just passed a significant milestone: its 150th birthday in print! As you may also have noticed, a number of print and online publications and websites have been marking the occasion in various ways; some I have bookmarked for sharing here, but haven't gotten around to as yet!

At the beginning of the semester (as I do every semester), I had asked you students to approach the book through as fresh (even naive) a perspective as you could muster, setting aside any preconceptions and trying to put yourself in the mind of an educated person in 1859 getting your hands on the book for the first time, hot off the presses. That, of course, is easier said than done; especially when in class we are surveying the latest discoveries and insights from evolutionary biology. How can one erase 150 years of scientific progress on the question from one's memory? I'm presuming, of course, that at least some of that accumulated wealth of knowledge from these 150 years has trickled down into your consciousness through your various classes (and despite perhaps your best efforts!). Well, I hope most of you have made it at least most of the way through the wonderful (if tedious to some modern eyes) book. If so, you will appreciate this classic review, reprinted by The Atlantic Monthly where it was first published in 1860 upon the book's maiden voyage across the pond to the American market, and written by Asa Gray, the eminent botanist, contemporary and close correspondent of Darwin himself. Here's a wikipedia excerpt about the two men:

Corresponding with Charles Darwin, Gray was helpful in providing information for the development of Darwin's theory on The Origin of Species. Gray, considered by Darwin to be his friend and "best advocate", also attempted to convince Darwin in these letters that design was inherent in all forms of life, and to return to his faith. Notwithstanding, Gray was a staunch supporter of Darwin in America, and collected together a number of his own writings to produce an influential book, Darwiniana. These essays argued for a conciliation between Darwinian evolution and the tenets of orthodox Protestant Christianity, at a time when many on both sides perceived the two as mutually exclusive.

That should prime you to go read the review, which is pretty sharp and honest, starting on this cautious note:

Novelties are enticing to most people: to us they are simply annoying. We cling to a long-accepted theory, just as we cling to an old suit of clothes. A new theory, like a new pair of breeches, ("The Atlantic" still affects the older type of nether garment,) is sure to have hardfitting places; or even when no particular fault can be found with the article, it oppresses with a sense of general discomfort. New notions and new styles worry us, till we get well used to them, which is only by slow degrees.

Wherefore, in Galileo's time, we might have helped to proscribe, or to burn had he been stubborn enough to warrant cremation-even the great pioneer of inductive research; although, when we had fairly recovered our composure, and had leisurely excogitated the matter, we might have come to conclude that the new doctrine was better than the old one, after all, at least for those who had nothing to unlearn.

Such being our habitual state of mind, it may well be believed that the perusal of the new book "On the Origin of Species by Means of Natural Selection" left an uncomfortable impression, in spite of its plausible and winning ways. We were not wholly unprepared for it, as many of our contemporaries seem to have been. The scientific reading in which we indulge as a relaxation from severer studies had raised dim forebodings. Investigations about the succession of species in time, and their actual geographical distribution over the earth's surface, were leading up from all sides and in various ways to the question of their origin. Now and then we encountered a sentence, like Professor Owen's "axiom of the continuous operation of the ordained becoming of living things," which haunted us like an apparition. For, dim as our conception must needs he as to what such oracular and grandiloquent phrases might really mean, we felt confident that they presaged no good to old beliefs. Foreseeing, yet deprecating, the coming time of trouble, we still hoped, that, with some repairs and make-shifts, the old views might last out our days. Après nous le deluge. Still, not to lag behind the rest of the world, we read the book in which the new theory is promulgated. We took it up, like our neighbors, and, as was natural, in a somewhat captious frame of mind.

and towards the end, warily acknowledges the "uncanny look" as well as the "mischief" of the book:

So the Darwinian theory, once getting a foothold, marches boldly on, follows the supposed near ancestors of our present species farther and yet farther back into the dim past, and ends with an analogical inference which "makes the whole world kin." As we said at the beginning, this upshot discomposes us. Several features of the theory have an uncanny look. They may prove to be innocent: but their first aspect is suspicious, and high authorities pronounce the whole thing to be positively mischievous.

Doesn't that make this your must read essay of the week?

Thursday, November 27, 2008

Tiktaalik in the Year of Darwin

A great video lecture for the holiday!

Wednesday, November 19, 2008

On Human Evolution

Is our species, Homo sapiens, still evolving? No doubt all of you have wondered about this at some point (unless you don't believe in evolution, in which case you have a different puzzle to scratch your heads over). And with human technology constantly coming up with ways to allay any selective pressures, it is easy to think that we've stopped evolution in its tracks as far as our own species is concerned. But have we, really? Is it even possible to pause evolution? Last month, Seed magazine had an interesting article, "How We Evolve" describing the state of current knowledge about human evolution and how modern genomics tools are helping to shed light on this question:

When the previous generation of life scientists was coming up through the academy, there was a widespread assumption, not always articulated by professors, that human evolution had all but stopped. It had certainly shaped our prehuman ancestors — Australopithecus, Paranthropus, and the rest of the ape-men and man-apes in our bushy lineage — but once Homo sapiens developed agriculture and language, it was thought, we stopped changing. It was as though, having achieved its aim by the seventh day, evolution rested. "That was the stereotype that I learned," says population geneticist and anthropologist Henry Harpending. "We showed up 45,000 years ago and haven't changed since then."

The idea makes a rough-and-ready kind of sense. Natural selection derives its power to transform from the survival of some and the demise of others, and from differential reproductive success. But we nurse our sick back to health, and mating is no longer a privilege that males beat each other senseless to secure. As a result, even the less fit get to pass on their genes. Promiscuity and sperm competition have given way to spiritual love; the fittest and the unfit are treated as equals, and equally flourish. With the advent of culture and our fine sensibilities, the assumption was, natural selection went by the board.

So what can genomics tell us?

John Hawks started out as a "fossil guy" studying under Milford Wolpoff, a paleoanthropologist who is the leading proponent of the faintly heretical multiregional theory of human evolution. Coming to genetics from such a background has perhaps given Hawks the stomach to wield unfashionable hypotheses. In December of last year, he, Harpending, and others published a paper whose central finding, that evolution in humans is observable and accelerating, would have been nonsensical to many geneticists 20 years ago. Up to 10 percent of the human genome appears to be evolving at the maximum rate, more quickly than ever before in human history.

Go read the rest of the story. Especially the frightening scenarios towards the end.

Friday, November 7, 2008

How plastic is your brain? Perhaps you'll find out in the Bio Colloquium today

Well, you will at least learn about neuroplasticity in species that do have more plastic brains then humans. As usual, the seminar will be in Science II, Room 109, starting at 3:00 PM. Be there!

Hormonal and environmental control of neuroplasticity

Dr. Christy Strand

Department of Biological Sciences

California Polytechnic State University

Abstract

Many people have the incorrect notion that the brain is a relatively static organ or that it can degenerate, but not grow. The study of neuroplasticity encompasses changes in the brain from the cellular and molecular level to the gross anatomical level (e.g. changes in the sizes of brain regions). In adult male songbirds, the brain regions that control singing behavior grow seasonally, providing a means to investigate the regulatory mechanisms and the functional consequences of adult neuroplasticity. Specifically, during the breeding season, these regions are larger than at other times of the year due to increases in neuron number and size or decreases in density. Numerous factors that change during the breeding season have been implicated in regulating the growth of these brain regions, most notably, testosterone (T), photoperiod and singing behavior. I use a comparative approach to investigate the effects of T, photoperiod, singing and other social or environmental factors on song control region growth and new neuron incorporation in the adult male songbird brain. I also investigate how environmental, physiological and hormonal factors affect neurogenesis and neuroplasticity in adult snakes and lizards. This integrative approach provides a more complete analysis of the contributions of various factors to the regulation of neuroplasticity in vertebrate animals.

When a Cutthroat meets a Rainbow

Submitted by Christopher Clapp for the Evolution class.

The introduction of a known species of rainbow trout into a native population of cutthroat trout and the consequences of their contact within their environments is the focus of this study. The interaction of these two species has resulted in their study of subsequent progeny shows hybridization of the two, and thus a decline of the natural populations of cutthroat trout. The implications of this hybridization will show throughout subsequent generations, considering what is known of the native species. Metcalf uses mitochondrial and nuclear markers to determine the levels of crossing of the two species based on the nature of homozygous or heterozygous allele category. These populations of hybridization were evaluated due to the known history of the streams being studied. Trout being separated by natural geographic restrictions such as natural waterfalls or by human chemical treatment conducted in the past forms for a basis of evaluation.

The successful progeny of hybridization between the two locations is evident; however there are differences between the chemically treated streams and the naturally restricted. Interestingly enough, results show that there is a trend of the cutthroat nuclear trout alleles being more prevalent beyond the upstream barrier as expected. The mitochondrial alleles were more prevalent within the hybrid or rainbow species within the areas that direct contact has been introduced within the natural barrier stream. Our study supports the notion that natural waterfall barriers provide a refuge for pure native cutthroat trout genomes across their range (Metcalf et al 2008). In the Cony Creek population, which was subject to chemical treatment in 1984, the nuclear markers were more prevalent within the cutthroat species. This bias toward the pure cutthroat is speculated to be due to the chemical treatment of the streams to eradicate the rainbow trout populations amidst restocking the cutthroat population (Rosenlund et al. 2001). Why is the case? The allele frequency distributions and disequilibrium values suggest that hybridization has been underway for longer in Cony Creek than in Graneros Creek according to Metcalf, et al (2008). I seem to feel that introducing a chemical treatment to an environment that focuses directly on one specific species allows for a re-founding of the native species. However, there findings show the invasiveness nature of the rainbow species. Over time the cutthroat nativity would be eradicated regardless of natural barrier or chemical treatment. This poses two major problems for the environment with regard to the natural species, and the changes of fish populations within streams. The introduction of new fishes for conservation strategies not only directly affect the native population, it affects the ecosystem among other animals within the environment as well. If an aggressive population of trout that is more successful than the native, the impact on resources for the community will also be affected; the environment will be in disequilibrium.

We seem to have two intrusions of the human hand into an environment, one for the introduction of the rainbow, and one to eradicate the rainbow trout species. The study shows that there is greater fitness among the hybrids. The cross between a rainbow trout female and a cutthroat male resulted in a shorter time to hatching and the progeny had a faster growth rate and a greater abundance of yolk at hatch and emergence than the hybrids of the reciprocal cross (Hawkins and Foote, 1998). Nevertheless, the two species form a system of fertility to study the hybrid selection based on natural selection and/or the effects of human based effects in the form of conservation strategies. What is this to say for the natural selection of the hybrid species or the difference between the two, and what are the effects of the introduction on the environment? Historically fishless lakes and streams have been associated with declines in amphibians, changes in invertebrate communities and changes in nutrient cycling (Knapp and Matthews, 2000). However, there is always something to be learned from the development of a new species. The selection and fitness over such a short amount of time is interesting to evaluate within the two species.

It seems to be that the rainbow trout are invading the natural species of cutthroat, and have an effect on the native species. Why are the rainbows so successful at invading this species? What are we to learn of the intrusion of populations by human hands? Either way, I agree with Metcalf in the capacity that the evaluation of the new hybrid species will give insight into long-term conservation strategies. It seems that if we limit the studies and only hold them as individuals there will always be contradiction of the results. Conservation methods and steps may be a bit naïve if you only consider one method to achieve one result. By not considering the whole picture, we are increasing our opportunity cost, and thus the potential for loss.

References:

Denise K. Hawkins, Chris J. Foote (1998). Early survival and development of coastal cutthroat trout (Oncorhynchus clarki clarki), steelhead (Oncorhynchus mykiss), and reciprocal hybrids Canadian Journal of Fisheries and Aquatic Sciences, 55 (9), 2097-2104 DOI: 10.1139/cjfas-55-9-2097

Roland A. Knapp, Kathleen R. Matthews (2000). Non-Native Fish Introductions and the Decline of the Mountain Yellow-Legged Frog from within Protected Areas Conservation Biology, 14 (2), 428-438 DOI: 10.1046/j.1523-1739.2000.99099.x

J. L. Metcalf, M. R. Siegle, A. P. Martin (2008). Hybridization Dynamics between Colorado's Native Cutthroat Trout and Introduced Rainbow Trout Journal of Heredity, 99 (2), 149-156 DOI: 10.1093/jhered/esm118

Rosenlund BD, Kennedy C, Carnowski K. 2001. Fisheries and the Aquatic management of Rocky Mountain National Park. (US Dept. of the Interior).

Tuesday, November 4, 2008

Endorsing a presidential candidate through the lens of Science

How can you argue (rationally) against this?

Far more important is this: Science is a way of governing, not just something to be governed. Science offers a methodology and philosophy rooted in evidence, kept in check by persistent inquiry, and bounded by the constraints of a self-critical and rigorous method. Science is a lens through which we can and should visualize and solve complex problems, organize government and multilateral bodies, establish international alliances, inspire national pride, restore positive feelings about America around the globe, embolden democracy, and ultimately, lead the world. More than anything, what this lens offers the next administration is a limitless capacity to handle all that comes its way, no matter how complex or unanticipated.

Sen. Obama's embrace of transparency and evidence-based decision-making, his intelligence and curiosity echo this new way of looking at the world. And that is what we should be weighing in the voting booth. For his positions and, even more, for his way of coming to them, we endorse Barack Obama for President of the United States.
[read the rest of the endorsement by Seed: Barack Obama for President]

And then, if you haven't already done so, go VOTE!!

Sunday, November 2, 2008

My Inferiority to Scrub Jays

Rudy Cerda confesses for the Birds & Reptiles class. Elsewhere, Claire Go has blogged about the same study!

As much as I like to think that I plan according to future needs, such as time management in order to write papers, study for exams, and even complete this blog, I know I can only operate under pressure. However, when planning for “essential” needs such as food or snacks, I save the best for last or at least hide some away in case I may need or want any later. For example, I’ll always leave my favorite flavor of candy last because I want that flavor to linger for awhile, or I’ll eat the crust first on a slice of pizza because I’d rather wait to take in the gooey, cheesy goodness on the other side of the piece... but enough of my planning for less than crucial things. Aphelocoma californica, better known as the western scrub jay, may exhibit planning for the future in perhaps a more critical way than I do.

According to the Bischof-Köhler hypothesis, only humans are able to disconnect themselves from their current motivation and plan for the future. Apparently other animals do not have crystal balls to predict their future needs and any future-oriented behaviors are due to either patterns of fixed actions or prompted by current motives. There have been previous studies involving rats and pigeons that have that have only supported the Bischof-Köhler hypothesis by the animals solving tasks involving the future, however, the “future” was only a very short time period. Also, primates have also shown the ability to take actions based on future consequences; however, the motives or reasons for the actions have not been differentiated.

Scrub jays are relatively abundant around campus and I frequently observe jays bouncing around with nuts in their beaks. Every so often I’ll see one that is particularly sneaky and decides to stash its food away as if its saying, “You’re not going take this from me,” or preparing for the budget cuts around campus (or perhaps they can sense the inevitable collapse of the economy!) that may take away their beloved seeds. Raby et al also noticed this behavior in western scrub jays and hypothesized that the jays store food based on anticipation of future need. They predicted that the jays would do this in an area in which they have learned they will be hungry and by storing a particular food item in a place where they know it will not be available.

To test this hypothesis, a total of eight western scrub jays were placed in two different compartments on alternate mornings for six days. In one compartment they were given breakfast and the other they were not. After this training, the birds were given food unexpectedly given food to either eat or store in the evening. If the birds were capable of planning for the future, they would store relatively more food if they were in the compartment in which they were not given breakfast because they would anticipate being hungry the next morning… psychics! And the results displayed their fortune-telling abilities as they stored significantly more food (more pine nuts than powdered nuts) in the compartment in which they had not received breakfast.

To ensure the hoarding of the pine nuts was not associated to a specific compartment, two different types of food were given; a specific food was given in a specific compartment and both types in a third compartment. If the jays had a preference of a certain food they would store more of the “other” food rather than the “same” food when offered to store the food away. The results supported the hypothesis of preferential storing food.

Often I find it hilarious when I see a jay hopping around with something in its beak, it hides the food and about 30 seconds later it’s looking for the food it just sneakily stashed away! Some planning if it can’t even remember where it put its food! In the Raby study, it was stated that the birds were slightly hungry, so perhaps those greedy jays around campus are just playing dumb because they aren’t hungry at that moment in order to fool everyone and plot their takeover of campus and my apartment complex! Well, it’s nice to know that my planning skills may be significantly inferior to a scrub jay’s.

Reference:

C. R. Raby, D. M. Alexis, A. Dickinson, N. S. Clayton (2007). Planning for the future by western scrub-jays Nature, 445 (7130), 919-921 DOI: 10.1038/nature05575

Saturday, November 1, 2008

Convergence of the Death Adder with Viperidae

Submitted by Brandon Williams for the Birds & Reptiles class.

In a study of the Australian death adder (Acanthophis antarcticus), a member of the Elapidae, Richard Shine observes the convergence of the snake with the Viperidae (Shine 1980). There are no vipers that live in Australia, yet the death adder resembles vipers much more so than other members of the elapids. Shine hypothesizes that the sit-and-wait ambush hunting techniques select for similar adaptations in vipers and death adders. Most elapids are more active searching foragers.

In many ways Shine shows how death adders are adapted in similar ways to vipers rather than their elapid cousins. Death adders feed mostly on ectotherms as juveniles and switch to endotherms as adults. Death adders have a shorter stouter body than most elapids and a pronounced head. A. antarcticus have a delayed sexual maturation and a corresponding slow growth rate. The delayed maturation probably evolved after the ambush hunting strategy, which tends to allow for high survivorship because that leaves less opportunity for predation on the snakes. A. antarcticus has a unique adaptation for ambush hunting which is completely absent in all other elapids, yet is found in nine different vipers. This adaptation is caudal luring; using the thin, yellow wriggling tip of their tail as bait for prey. All of these adaptations point to convergence of the death adder with vipers. The reason for this is the ambush hunting technique.

Shine also posits that because just over half of mature females were found not to be reproductive that female death adders reproduce every other year. He was probably correct, however there could be some genetic or another unseen reason why many of the females were non-reproductive. Testing his hypothesis could be done. He could collect live female specimens of mature size during the breeding season, tag them with a number, noting whether they were reproductive or not, and let them go. Then over the next few breeding seasons he could collect female death adders that had been tagged and note whether the ones that were specifically reproductive last season were non-reproductive the following season. Over a few seasons he could see how consistent the data was with his every other year hypothesis.

Reference:

Shine, R. 1980. Ecology of the Australian Death Adder Acanthophis antarcticus (Elapidae). Pp. 281-289. Evidence for Convergence with the Viperidae. Herpetologists' League.

Wednesday, October 29, 2008

A Bite of Beta-Carotene for Better Twitterpation

Submitted by Pedro Garcia for Evolution

Birds, birds, and more birds, with over 10,000 species of birds well known and classified, one can get an array of different colors which would make even the most non-bird lover’s staring in awe. With some species having such intricate combinations of reds, yellows, greens, and blues, (such as the scarlet macaw of South America) one might ask, “Why do they have such vibrant and magnificent plumage?” (or something along those lines). It’s a well known fact that skin and feather color (yellows and reds) is linked with carotenoids in the body. One well known example is the Caribbean flamingo, known for its brightly reddish/pink color. This species of bird gets its color from the high intake of beta-carotenes obtained from its diet of crustaceans and algae. But why? What good is it to be so brightly colored? One might even think that such bright colors would be a sort of bull’s eye for predators as if saying “Hey, you…the one with the sharp teeth…I’m over here!” Well, in short, it can all be explained by loosely quoting the hip hop song… “it’s all about sex, baby!”

That’s right, ongoing research has been linking brightly colored plumage in birds to…well, sex! This is the not-so-PG stuff that Darwin didn’t really talk about in his book (at least not directly), however it is merely the process of evolution at work. Researchers Negro, et al, (2002), have gone even more in depth concerning the correlation of plasma carotenoid-dependent skin color in relation to sexual selection. Their work consisted of analysis of brightness of color, not in the feathers, but, in the cere, lores, and tarsi of the small falcon the American Kestrel (Falco sparverius) along the time scale of mating season to hatching of offspring. As stated in the article, research has shown that color of plumage in birds does have an effect on sexual selection in brightly colored birds (Negro, 2002). As stated earlier, the brightness of plumage (specifically reds and yellows) is dependent on the amount of carotenoids found in the body; and beta-carotene is taken in directly from food source. Simply put, female birds choose the male with the brightest plumage because he is the one that can successfully obtain the most food, thus passing on the “better” genes to the offspring. As said before, it’s the process of natural selection at work.

Although there has been much research on sexual selection and plumage color, this article delves in even further and tries to find a correlation with skin color in birds as a function of sexual selection. It seems that, as hypothesized before, there is a brighter skin hue during the mating season. However, what came next seemed to be of even greater interest. It seems that, at least among American Kestrels, the “brightness” of the skin color began to fade as soon as the mating season ended. This was directly linked with a reduction in plasma-carotenoid levels (Negro, 2002). It is believed that the reduction occurs as a trade-off between sexual selection (during mating season) and maintaining better health (post-mating season). Since the bright coloration is no longer needed after mating, it would seem that a reduction in plasma-carotenoids would allow for the carotenoids to assist in other health-related body functions (such as anti-oxidants aiding in the reduction of oxidative damage by free radicals).

One concern I have with research is the methodology used for the experiments. All subjects were captive Kestrels from the “Avian Science and Conservation Center of McGill University, Canada…” which were fed a consistent diet of “…day-old cockerels” which were carotenoid-rich (Negro, 2002). This brings up my concern that the Kestrels were not mimicking natural processes, thus adding, in my eyes, a great amount of tolerance and bias to the results. It should be noted that the author does state that they have “previously shown that variation in plasma carotenoids during the mating period (April) was not attributable to diet, parasites or androgen levels” (Negro, 2002). Ideal settings that would eliminate this tolerance would include plasma collection of marked Kestrels in the wild throughout a series of mating and fledging seasons.

References

J. J. Negro, G. R. Bortolotti, J. L. Tella, K. J. Fernie, D. M. Bird (1998). Regulation of integumentary colour and plasma carotenoids in American Kestrels consistent with sexual selection theory Functional Ecology, 12 (2), 307-312 DOI: 10.1046/j.1365-2435.1998.00176.x

On McCain/Palin's appalling contempt for science and learning

Trust Christopher Hitchens to lay it out in choice words:

In an election that has been fought on an astoundingly low cultural and intellectual level, with both candidates pretending that tax cuts can go like peaches and cream with the staggering new levels of federal deficit, and paltry charges being traded in petty ways, and with Joe the Plumber becoming the emblematic stupidity of the campaign, it didn't seem possible that things could go any lower or get any dumber. But they did last Friday, when, at a speech in Pittsburgh, Gov. Sarah Palin denounced wasteful expenditure on fruit-fly research, adding for good xenophobic and anti-elitist measure that some of this research took place "in Paris, France" and winding up with a folksy "I kid you not."
It was in 1933 that Thomas Hunt Morgan won a Nobel Prize for showing that genes are passed on by way of chromosomes. The experimental creature that he employed in the making of this great discovery was the Drosophila melanogaster, or fruit fly. Scientists of various sorts continue to find it a very useful resource, since it can be easily and plentifully "cultured" in a laboratory, has a very short generation time, and displays a great variety of mutation. This makes it useful in studying disease, and since Gov. Palin was in Pittsburgh to talk about her signature "issue" of disability and special needs, she might even have had some researcher tell her that there is a Drosophila-based center for research into autism at the University of North Carolina. The fruit fly can also be a menace to American agriculture, so any financing of research into its habits and mutations is money well-spent. It's especially ridiculous and unfortunate that the governor chose to make such a fool of herself in Pittsburgh, a great city that remade itself after the decline of coal and steel into a center of high-tech medical research.
...
With Palin, however, the contempt for science may be something a little more sinister than the bluff, empty-headed plain-man's philistinism of McCain. We never get a chance to ask her in detail about these things, but she is known to favor the teaching of creationism in schools (smuggling this crazy idea through customs in the innocent disguise of "teaching the argument," as if there was an argument), and so it is at least probable that she believes all creatures from humans to fruit flies were created just as they are now. This would make DNA or any other kind of research pointless, whether conducted in Paris or not. Projects such as sequencing the DNA of the flu virus, the better to inoculate against it, would not need to be funded. We could all expire happily in the name of God. Gov. Palin also says that she doesn't think humans are responsible for global warming; again, one would like to ask her whether, like some of her co-religionists, she is a "premillenial dispensationalist"—in other words, someone who believes that there is no point in protecting and preserving the natural world, since the end of days will soon be upon us.

Go read the rest. Then VOTE (sorry I can't) to make sure these people aren't in charge of your country for much longer!

Note, however, that common usage of names notwithstanding, Drosophila are not fruit flies (as you should know even if Hitchens doesn't - if you've taken Entomology). Palin was referring to a study of the olive fruit fly (pictured above), which is a true fruit fly (Tephritid), as well as a serious crop pest right here in California. Which makes her remarks even more bizarre because she was attacking applied research of considerable economic significance - research that many a farmer might care about even more than us urban elites pursuing basic research!! Clueless in so many ways...

[Hat-tip: onegoodmove and Evolgen]

Monday, October 27, 2008

Marking a quarter century of living and fighting with HIV

Scientific American has a special report out on: HIV--25 Years Later]. Check it out! Here's the editor's introduction:

In 1983 and 1984 scientists established that HIV (the human immunodeficiency virus) causes AIDS, which had recently begun cropping up in gay men in California and New York. The discovery quickly led to predictions that a preventive vaccine would soon be on tap. Similarly, in 1996, after powerful drug combinations began forcing HIV down to undetectable levels in the blood, prominent HIV researcher David D. Ho of the Rockefeller University voiced optimism that attacking the virus early and hard could prove curative.

Yet neither a vaccine nor a cure has materialized. Indeed, the most promising vaccine prospects have failed. And when aggressive treatment stops, the wily virus comes roaring back.

Where do we go from here? Scientific American asked two leading HIV researchers to address the biggest scientific challenges facing the field today: Is finding a vaccine even possible? And what, exactly, would it take to rid a person’s body of HIV and thus effect a cure? Their frank, thought-provoking answers follow.

And if you want to read a first hand account from the early days of what it was like to deal with the beast in the field, my favorite is Abraham Verghese's memoir of the period he spent as a doctor in the South (not those coastal cities) when HIV first hit small-town communities: My Own Country: A Doctor's Story.

Darn those scientists, confounding our politics again!

Unbelievable!! This is the leadership we are supposed to look forward to?!

As someone who came to the US because of the opportunities this country offered to pursue scientific research, and having seen science get bipartisan lip service (at least) over the past 4 presidential election cycles (when I have been here), despite the decline in science funding over the past 8 years, I find it really bizarre to see this "team of mavericks" tilting against the windmills of science in this fashion! First it was McCain railing against "pork-barrel" earmark funding to study the genetics of grizzly bears (a very successful project, btw, that he had actually voted for, before turning it into a convenient flogging-horse on the campaign trail), and now Palin takes on the iconic model organism of modern genetics, Drosophila!! Talk about clueless chutzpah, bashing research on the very organism which has yielded, among myriad other insights, important clues about autism, the cause she claims she would fund by cutting off these "earmark" projects!! But, as has been clear from the day she joined the ticket, and as Rachel Maddow demonstrates yet again, this hockey-mom continues to operate in a completely irony-free zone - how can one make fun of her when she embodies the joke so completely? (remember how people chuckled when someone initially suggested that she had foreign policy expertise because of Alaska's proximity to Russia; until she actually took that line seriously and ran with it?)

Science - cutting-edge basic science - has surely been one of the defining characteristics of this country's global leadership over the past half-century or more, no?! Why do these "mavericks" now suddenly think it is ok to throw that away, and that they will win more votes if they bash science and scientists? I've wondered about the curious dichotomy in this culture, where science and technology provide the basis of so much of everyday life, yet science and scientists, and intellectuals in general, are feared/reviled as nerds/dangerous elitists. Is the anti-intellectual strain in this society so strong that McCain/Palin can drum up a few more votes to win this election by continuing to bash science, and further entrench the age of american unreason? Please tell me that is not the case, that things haven't gone that far wrong... or should I be packing my bags as another soon-to-be-unwanted scientist who has been wasting his life and taxpayer money studying birds??!! While remaining a foreigner, to boot!!

Sunday, October 26, 2008

On the early evolution of cells

Submitted by Brandon Williams for the Evolution class.

In this article, Carl Woese provides a theory on the early evolution of cells. Woese posits that it is necessary to go beyond classic Darwinian thinking of Vertical Gene Transfer (parent to offspring). He believes that Horizontal Gene Transfer (HGT) played a more crucial role in the early development of cells; that is until each of the three branches of life (Bacteria, Archaea and Eucarya) reached their Darwinian Thresholds. This threshold is a point where the cells of random RNA and proteins have finally reached a level of complexity that they have become a “species” and Vertical Gene Transfer can take over. Before that, cells traded genetic material with each other, evolving as a community.

I commend Woese for attempting to push us past the thought of endosymbiosis. While endosymbiosis may have occurred, the two cells that combined had to have been fully evolved cells that functioned without each other before the joining. Careful consideration to his theory needs to be taken to understand how much of translation and transcription was evolved before bacteria, archaea, and eukaryotes emerged. The wide spread similarities and differences point to some truth in this.

Woese may have a better explanation than endosymbiosis as to how archaea, bacteria and eukaryotes evolved past their Darwinian threshold through HGT; however, he still cannot explain how those cells could initially evolve the genomes (albeit small) to trade parts with in the first place. He posits that translation existed before transcription or genome replication. RNA dominated and proteins were made, transcription completed evolution after each Darwinian threshold, and genome replication came third. I find it interesting yet hard to believe that nucleotides formed by themselves, without a metabolic pathway already in place, and in enough numbers to form RNAs capable of translating proteins. Enough amino acids would have to exist also and Woese gives no explanation for their appearance or the fact that they are conveniently in close proximity to the RNAs. I also find it hard to believe that such an incredible amount of nucleotides and amino acids existed to support enough primitive cells containing RNA and protein that were able to trade with each other, and that these ancient cells would survive long enough to reach a Darwinian threshold.

In conclusion, Carl Woese’s theory could have serious implications on our idea of the early evolution of cells when before we were content to recite “endosymbiosis” and leave it at that. However it still leaves us glaring at what we don’t know and may never know.

Reference:

C. R. Woese (2002). On the evolution of cells Proceedings of the National Academy of Sciences, 99 (13), 8742-8747 DOI: 10.1073/pnas.132266999

Socially learned foraging behaviors in wild black bears

Andrew Mora offers a review of the Biology department seminar by Rachel Mazur.

The American Black Bear, Ursus americanus, is currently the only species of bear in the state of California. In a fascinating presentation by Rachel Mazur, pictures and videos were used to depict the beauty of these bears in their natural and not so natural environments; the latter being bears foraging for food in developed areas of the national parks including getting food out of trash cans, cars, etc.

According to Mazur, these bears are especially hungry during the months of March and April. During this time, a bear is either termed by Mazur to be a wild foraging bear, which consists of eating grasses, roots, insects from shredding logs etc., or they can be food conditioned bears, which consist of getting their nutrition from developed areas, or humans.

Research by Mazur finds that bears have traits for social learning and the most critical times of a bears learning process is during the first year when they are in constant contact with their mother (Mazur, 2008). Three separate hypotheses were compared to describe how these bears are learning to become food-conditioned to developed areas. The first is that bears inherit these behaviors from their mothers and can be predicted (Mazur, 2008). The others include bears learning individually (that is, without the help of the mother) and transmitted learning from sow to cub (Mazur, 2008).

The methods used for this experiment were efficient in that homogeneity was taken into consideration. Therefore five variables were taken into consideration including park, sow identity, sow behavior, rearing method and cub outcome (Mazur, 2008). The two national parks which Mazur encouraged everyone to visit include Sequoia National Park and Yosemite National Park. From showing clips of a movie on this research, it was evident that many years of hard work by numerous staff was done to work with these bears and monitor their statuses.

Mazur stated that she was very pleased with the results that they came across. An easy to read table of her results shows the number of sows that they started with (23 food conditioned and 9 wild), the rearing methods of these sows (rearing in wild or food-conditioned rearing), and the outcome of the cubs once separated from their mothers (Mazur, 2008).

Conclusions made by Mazur asserted that rearing method had a highly significant effect on the cub outcome (Mazur, 2008). If a cub was reared food-conditioned, it was much more likely to be food-conditioned once separate from its mother. That being said, the last hypothesis stated by Mazur was seen to be the most accurate: that bears become food-conditioned through social learning.

In both seminar and paper, Mazur stated that there are numerous implications for the work that has been done. She posed a question to the room regarding the bear’s possibility of creating culture and even tradition in our national forests with these new food-conditioned characteristics (Mazur, 2008). What I found beneficial in this work is the implication that food-conditioning in developed areas in our national forests do not necessarily imply adaptive strategies of these Ursus americanus, but may very well be falling into an ecological trap (Mazur, 2008). I also found it interesting for her to note that science and management have recently become less taboo as a pair in the scientific world.

Reference:

R MAZUR, V SEHER (2008). Socially learned foraging behaviour in wild black bears, Ursus americanus Animal Behaviour, 75 (4), 1503-1508 DOI: 10.1016/j.anbehav.2007.10.027

Friday, October 24, 2008

Lizards Showing Some “Leg”

Submitted by Cindy Hua for Evolution

Most of us think that evolution in species take several generations to thousands of years to occur. However, how about if I say in one generation’s time there is a significant change in morphology? Jonathan Losos and his team of researchers from Washington University, St. Louis has found a peculiar lizard that is evolving in a tremendous rate. The brown anole, a Caribbean native lizard, spends most of its day hunting on the ground. One of its main predators is the curly-tailed lizard.

As we all know from our evolution class, a chain of islands sets up a great opportunity for parent species to change significantly. Since the Bahamas are home to the brown anole, natural selection will most likely to occur if there is a change in predator population. Losos has tested his hypothesis that with the introduction of more curly-tailed lizards into the main island, the brown anoles are under the influence of selection pressure change (Losos, et. al, 2006). When brown anoles sense danger of increasing populations of curly-tailed lizards, it flees towards trees and stay away from the ground activities for a few generations.

After a year’s experiment, Losos discovered that the brown anoles are experiencing a change in leg morphology. In the first six months of his study, the anoles originally had long legs, which enable them to outrun the predators. However, six months later, the survivors had drastically shorter legs, which permit them to hide in narrow crevices and climb in trees. Losos noticed that within a single generation, the anoles went to quick reversals in selection pressure (Losos, et. al). The behavior of the lizards changed, as they prefer treetops than the ground. Here we see natural selection at its finest.

Over several generations down, the continuing threat of curly-tailed lizards will force the anoles population to evolve shorter and shorter legs. However, I find it hard to believe that brown anoles can evolve in one generation at such a fast pace. Perhaps through time the longer legged anoles died off and Losos found mostly shorter legged since it was able to survive and reproduce.

The quick reversal of evolution by means of selection pressure is quite interesting. The brown anoles started with long legs to outrun its predators but discovered it to be a hindrance as it cannot bend its legs to hide in crevices. It preferred to have shorter legs to save energy and it is easier to live in trees away from the main predator. The anoles do not have a use of long legs anymore so it does not have to evolve back. For example, ostriches, emus, and kiwis all are flightless birds yet they have small wings. Their ancestors were flying species, but, through time, with fewer predators to run away from, they probably foraged on the ground more. Over generations, they most likely could adapt better on land and did not need developed wings for flight. That is why they evolved long, strong legs for running and scratching for food. I believe this is similar to what is occurring to the brown anoles. Their ancestors must have evolved longer legs to run away from predators. however, current species reverted to shorter legs when selection pressure changed. Although I believe the leg lengths did change because of pressure, I find it hard to believe this had all occurred in one generation.

Reference:

J. B. Losos, T. W. Schoener, R. B. Langerhans, D. A. Spiller (2006). Rapid Temporal Reversal in Predator-Driven Natural Selection Science, 314 (5802), 1111-1111 DOI: 10.1126/science.1133584

Development and Divergence of Canid Morphology, A Critical Review

Submitted by Tara Clever for the Evolution class.

When considering the comparison, it is astonishing that toy poodles belong to the same family as wolves: Canidae. Even more interesting is the observation of the divergence of domestic dogs from wolves. Robert K. Wayne approaches this topic with his paper “Limb Mophology of Domestic and Wild Canids: The influence of Development on Morphologic Change.” His primary objective was to determine whether allometry as an index of development and function is the same in domestic and wild canids. (Wayne 1986)

Thursday, October 23, 2008

Cellular scaling rules and primate brains - revisited

Kelsey Faria blogs about a paper, earlier reviewed here, for her contribution to the Evolution class.

The order of Primates is known for a variety of species that are energetic, inquisitive, social, and intelligent. Whereas the order of Rodentia typically lack the range or number of skills that primates encompass. Theses differences seem to put these two orders in completely different categories, although species in each order have relatively similar brain sizes. So the question arises what could be different about their brains that it affects their behavior? The question raises the possibility that primate brains differ from rodent brains in their cellular composition (Herculano-Houzel et al 2006).

The authors examined the cellular scaling rules for primate brains and show that brain size increases isometrically as a function of cell numbers. This isometric function is in contrast to rodent brains. Rodent brains have the ability to increase faster in size than in numbers of neurons. As a result of the linear cellular scaling rules, primate brains have a larger number of neurons than rodent brains of similar size (Herculano-Houzel et al 2006). In all probability this would give primates an advantage over the rodents which may explain the richer behavioral repertories and better cognitive abilities (Herculano-Houzel et al 2006).

Brain size fluctuates across mammalian species, and several studies have focused on finding any shared regularities behind brain morphology and cellular composition across species with different brain sizes. With these regularities this leaves room to discover new hypothesis about the underlying development and evolution of the brain. Studies have proven that animals from different species differ in their behavioral repertoires, and one would assume differences in cellular composition of the brain

The authors conducted an analysis in which cellular scaling rules were applied to rodents and primate brains. They concluded that the average neuronal size is larger in larger brains, whereas the average non-neuronal cell size remains comparatively stable. They also discovered that the neuron ratio increases with increasing brain size (Herculano-Houzel et al 2006).

With the information collected through this analysis the authors were interested in applying the scaling rules to other mammalian orders. There main goal was to set rules that can be applied to all brains and possibly reflect characteristics from a common ancestor which would conclude why there is a phylogenetic variance across orders. They were particularly interested in cellular scaling differences that might have arisen in primates. If the same rules relating numbers of neurons to brain size in rodents also applied to primates, a brain comparable to ours, with approximately 100 billion neurons, would weigh approximately 45 kg and belong to a body of 109 tons, about the mass of the heaviest living mammal, the blue whale (Herculano-Houzel et al 2006).

Inevitably their study indicates that there must be scaling differences between rodent and primates due to their behavior relative to similar brain size. The authors used the isotropic fractionators, which is a non-stereological method, which estimates the total number of neuronal and non neuronal cells in the cerebral cortex, cerebellum, and remaining structures of the brain (Herculano-Houzel et al 2006). They examined across six species of the order Primata, from Callithrix to Macaca, and in the closely related tree shrew, which is in the order Scandentia.

From the results gathered the authors concluded that the cellular scaling rules for primate brains differ from those of rodents. There was a distinct difference between the primate brains and rodent brains, primate brains do not hyper scale as they gain neurons, as rodent brains do. Primate brains also increase in size according to their number of neuronal cells which means that the average neuronal cell remains constant. The rodent brains increase in size faster than they gain neurons, which results in a increasing in the average neuronal cell size. When looking at neuronal densities they remain stable in primates and they tend to decrease in rodent brains. Primate ratios of non-neuronal neuronal cells to Mbr (brain mass) do not correlate although rodent’s ratios do.

The authors also included the tree shrews included in the experiment did not alter the results. Therefore the tree shrews are in fact a close relative of the primates and they to conform to the primate scaling rules.

Some implications for humans according to the data are that larger brains do not have a larger relative number of neurons in the cerebral cortex. From their results both the cerebral cortex and the cerebellum represent fractions of brain mass but do not differ significantly with an increase in brain size. Although, relative cortical size is seen to increase significantly with increasing brain size when larger species, such as great apes and humans, are considered (Herculano-Houzel et al 2006). It will be interesting to see if these scaling rules will apply if and when the addition of apes and humans are included in the experiment. A primate brain containing 100 billion neurons would be expected to weigh about 1,450 g and belong to a body of 72.7 kg, values that match the average mass of a human’s brain and body. This would conclude that humans and their brains are in fact isometrically scaled up versions of a common primate plan (Herculano-Houzel et al 2006).

Reference:

Suzana Herculano-Houzel, C. E. C., Peiyan Wong, and Jon H. Kaas (2006). "Cellular scaling rules for primate brains." Proceedings of the National Academy of Sciences 104(9): 3562–3567. doi: 10.1073/pnas.0611396104.

On glaciations, climate change, and pleistocene isolated fish

Raj Kotagiri offers his perspective on a Biogeography class discussion.

This is a review of our discussion several weeks ago about the Glaciation and Pleistocene periods. There were four major periods in the history of Earth during glaciation period and probably the most important of these is the second period that occurred some millions of years ago between 850 Ma to 635 Ma during the late Proterozoic Age. It was suggested that during this age Earth was covered completely in ice and then led to the Cambrian Explosion which has been responsible for diversification of multi-cellular life during this era.

The current period of constant glaciations in Pleistocene epoch from 1.8 million years to 10,000 years BP where the present continents were positioned and the plates on which these continents rested have not rotated more than 100 km since the start of this period. Repeated glacial cycles have described the climate of Pleistocene period pushed to 40th parallel in some places. 30% of the surface of the Earth has been covered by ice at its highest extent. Also, there was a zone of permafrost that extended from southern edge of glacial sheet of North America to Eurasia. The average annual temperatures of the ice and permafrost were -6˚C and 0˚C respectively.

One of the papers we discussed in class was “Global heat budget, plate tectonics and climate change” (Harris, 2002). This paper stimulated curiosity and discussion among the students in class. We arrived to the following conclusions about climate change on Earth from the paper and discussion.

The Earth’s surface temperature has fluctuated since past 2000 Ma.
Individual locations on Earth have undergone long-term change in temperature at different times and in different places.
We discussed new evidences concerning the difference in heat absorption by land and water; such as, the transport of excess heat pole ward from the tropics and the change in distribution of land and sea resulting from plate tectonics. These evidences explain the major fluctuation in the geological record-setting temperatures measured during last 350 Ma. However, these evidences create confusion since they are not supported by sufficient background data.
he paper also dealt with various controls which resulted in the climate change on the Earth’s surface.

First control dealt with changes in the distribution of land and sea due to plate tectonics. This explains the major temperature fluctuation (>25˚C) around the globe in the last 350 Ma.
Second order control was large scale changes in ocean currents and thermohaline circulation (15-25˚C).
Third order control was Milankovitch orbital cycle producing variations in the air temperature by order of 10˚C.
Fourth order control was massive volcanic eruptions and how changes in carbon dioxide production caused minor perturbations (<5˚C).

The take home message of our discussion was: the Earth's climate change was influenced by many factors; some of which act independently, while others acted interdependent with each other. The process of climate change was a gradual process which took many millions of years to see any significant change in climate. This change in temperature and climate, at different locations of the Earth, resulted in the geological distribution of various types of habitats on Earth.

The second paper we discussed in class was “Pleistocene isolation in the northwestern pacific marginal seas and limited dispersal in marine fish, Chelon haematocheilus (Temminck and Sclegel, 1885)” (Liu et al, 2007). This paper deals with three marginal seas: the Sea of Japan, East China Sea and South China Sea. During the period of Pleistocene glaciation when the whole earth was mostly covered by ice, the populations of living organisms were isolated in the seas.

We discussed the hypothesis that the rise of post glacial sea level resulted in the homogenization of the population by high disperse potential. To test this hypothesis, researchers used Chelon haematocheilus as the model organism. This fish belongs to the Mugilidae family, and is present in shallow coast water as well as freshwater regions in north Japan through the Korean Peninsula, and to the coast of China South. The early life history characteristics indicate that potential larval dispersal of C. haematocheilus is high. If C. haematocheilus larvae could travel on the currents, the connectivity should be high among populations within this region. The distribution and biological characteristics of C. haematocheilus make it a good subject to test the homogenization hypothesis.

Molecular analysis revealed three lineages which might have diverged in the three marginal seas during Pleistocene low sea level. Analysis of molecular variance and population statistics revealed significant differences in genetic structure among populations of the marginal seas. The outcome of the above analysis revealed that gene flow in C. haematocheilus is far more restricted spatially than predicted by the potential dispersal capabilities of this species. These results provide evidence for strong genetic divergence among these fishes in the marginal seas of the Northwestern Pacific, which coincides with expected pattern of vicariance due to sea level changes during the Pleistocene.

In order to support the above hypothesis further investigation should be done on other species of the same region.

Stuart A. Harris (2002) Global Heat Budget, Plate Tectonics and Climatic Change. Geografiska Annaler. Series A, Physical Geography, 84:1-9

JIN-XIAN LIU, TIAN-XIANG GAO, SHI-FANG WU, and, YA-PING ZHANG. (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology 16:275-288. DOI: 10.1111/j.1365-294X.2006.03140.x

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