Friday, September 23, 2011

Two TT jobs in Biological Sciences at University of Cincinnati

Two Tenure-Track Faculty Positions in the Department of Biological Sciences, University of Cincinnati (, at the Assistant level.  We seek individuals studying (1) SENSORY BIOLOGY, using cellular/molecular approaches to understand the function and/or evolution of sensory systems, which complement existing strengths in Sensory Biology, Behavior & Evolution; (2) PHYSIOLOGY, investigating responses of organisms to environmental stress at the molecular, cellular or ecosystem level.  This position will complement existing strengths in Environmental Change & Biological Resilience.  Applicants must hold a Ph.D. and have postdoctoral experience. Successful candidates will build an outstanding, externally-funded research program, contribute to undergraduate and graduate teaching, and fulfill service duties.  Apply online at (Positions 211UC1722, 211UC1719) by submitting cover letter, curriculum vita, and statements of research interests and teaching philosophy. Send three letters of recommendation and three representative reprints separately (PDF preferred) to:  Review of applications will begin November 15, 2011 until the position is filled.  The University of Cincinnati is an affirmative action/equal opportunity employer.  Women, minorities, disabled persons, and Vietnam Era and disabled veterans are encouraged to apply.

Friday, March 25, 2011

Of Mice and Mountains

If you have ever ascended Mount Everest, or even visited a city of high elevation, then you are personally aware of the physical discomforts, such as chest constriction, labored breathing and dizziness, which can result upon entering a high altitude, hypoxic (low levels of oxygen) environment.  We all know that oxygen is required for life (with the exception of those extremeophiles living deep underwater or in hot geysers somewhere).  Going only a few minutes without it can lead to permanent brain damage in newborn babies and adult humans alike.  But what about in environments with low levels of oxygen? What happens on a biochemical level to allow organisms to persist in such alpine environments?  Well, Storz et al. (2008) have recently identified specific amino acid changes in hemoglobin genes that account for differences in high and low altitude adaptation in deer mice populations.  Before delving further into this research, however, some background information is warranted: first, considering hemoglobin function in most vertebrates, and second, summarizing what is known to date about high altitude adaptations.

In ideal conditions, that is, at sea level, oxygen concentration is approximately 21%, which, in healthy individuals, saturates hemoglobin (the oxygen-binding protein found in red blood cells). Hemoglobin transports oxygen and other gases from the lungs to various tissues throughout the body, where the oxygen is then released for cell processes.  Hemoglobin in turn carries carbon dioxide, a waste product, back to the lungs for expulsion.  At sea level, our saturated hemoglobin molecules can transport the maximum amount of oxygen throughout the body and cellular mechanisms can function ideally.  This does not remain true when we ascend to higher elevations, where less oxygen is available. Eventually, we may acclimatize to these high altitude conditions, but what about organisms that permanently inhabit such an environment? Various species of plants, animals and microbes inhabit and thrive in environments thousands of feet above sea level. Adaptations must exist to allow them to persist in these conditions. Clearly, something must be different between sea level-dwelling creatures and alpine ones.

Hemoglobin represents a likely source of variation underlying altitude adaptations to low and high elevations as it is directly linked to oxygen transportation and utilization.  This idea was extensively investigated in the 1970s and 1980s by L.R.G. Snyder and M.A. Chappell, who studied hemoglobin biochemistry and genetics. From these efforts, we now know that the variations in blood chemistry at different elevations are due to a complex hemoglobin polymorphism (more than one form of the same thing). Specifically, Chappell and colleagues linked differences in blood oxygen affinity (the ability of oxygen to bind to hemoglobin) with variation at two gene duplicates that code for a hemoglobin subunit.  Both gene duplicates are polymorphic for two main classes of protein alleles (different forms of a gene), which we can call “A” and “B.”  The three combinations of these two allele types correspond to different blood oxygen affinities: mice with two “A” alleles exhibit a high oxygen affinity, “BB” mice exhibit a low affinity, and mice with both “A” and “B” (known as a double heterozygote) have an intermediate affinity. Additionally, mice with the high affinity genotype (combination of alleles for a certain characteristic) performed best at high elevations under hypoxic conditions, but poorly at sea level; and vice versa for mice with the low affinity genotype.  Mice with the heterozygote genotype were intermediate in oxygen affinity and performance. So we know that specific hemoglobin genes differ between high and low altitude populations, and that these differences confer fitness advantages: in this case, variation in the physiological performance of the mice. With this extensive empirical background and modern molecular genetic techniques, researchers are now address the specific molecular changes responsible for these physiological adaptations to high altitude environments.

In a 2008 paper published in PLoS Genetics, Jay Storz et al. investigate just that: the genetic mechanisms of alpine adaptation in the wide-ranging deer mouse, Peromyscus maniculatus.  The deer mouse is an excellent species in which to study high altitude adaptation, since it has the widest vertical range of any mammal in North America, spanning from below sea level (Death Valley, CA) to alpine environments higher than 4,300 meters.  At these extreme heights, the partial pressure of oxygen (pressure exerted by oxygen alone) is only 55% of that at sea level; thus the deer mouse experiences vastly different oxygen environments. In this paper, the authors aim 1) to identify the specific genetic mutation responsible for hemoglobin divergence across varying altitudes and 2) to test for evidence of diversifying selection (different traits favored in different environments) between high and low altitude populations.

To do this, the authors collected 41 mice from three areas along an altitudinal transect spanning nearly 4,000 vertical meters and across a linear distance of 547 km, from the lowlands of Kansas to the mountains of Colorado. From the mouse blood, they cloned copies of adult α-globin (one of the protein parts of hemoglobin), and by examining amino acid (organic building blocks of proteins) variation, were able to identify six amino acid substitutions (a swap of one amino acid for another) that distinguish the two gene duplicates discovered in the earlier research mentioned above. Hemoglobin, as a protein, is composed of a linear sequence of amino acids, which, if altered, may affect the properties of the molecule, including oxygen-binding affinity. Of the six substitutions, the authors identified one of significant functional consequence, which is referred to as 58(E7)HisàGln, but we will just call it E7 (His and Gln represent two distinct amino acids). In all mammals studied to date, E7 serves a critical role in iron-oxygen binding in hemoglobin. In humans, this substitution results in increased oxygen affinity in low oxygen environments.

The authors subsequently propose that, being found in both high and low altitude environments, deer mice have BOTH E7 forms (one with His and one with Gln) present in their blood, each with a unique oxygen binding affinity, and some mechanism to regulate the ratio of one E7 form to the other in response to metabolic demand. Why is this so interesting? Well, the possession of multiple hemoglobin forms has been documented in only one other mammal, the Yak, which lives high in the Tibetan Plateau.  Also, these different forms of the same protein represent functional divergence (genes duplicate and then diverge in function), rather than the concerted evolution (pair of genes evolves in concert) that was demonstrated in other mammal systems. This alone is pretty interesting, but the authors also wanted to test for evidence of the predicted mode of selection, diversifying selection, responsible for this difference. 
To do this, the allele frequencies at the two genes were compared between high and low altitude individuals; significant polymorphisms were observed that fit with a model of diversifying selection.  Continuing down the road of diversifying selection, the authors also found a significant excess of linkage disequilibrium (when alleles group in a nonrandom manner), and higher levels of altitudinal differentiation in the two genes of interest than in a group of unlinked nuclear loci (locus=gene site) that were used as a neutral comparison.  Both findings are consistent with a model of diversifying selection.  The authors then identified five replacement polymorphisms based on two things: 1) a high value of site-specific differentiation (between low and high elevations) and 2) a high frequency of the derived allele at high elevations. Of these five candidates, the amino acid substitution 64(E13) AspàGly (E13 for our sake) was singled out and predicted to increase oxygen-binding affinity; in fact, this is the case in human hemoglobin (The E13 in deer mice is shown in the image to the right). In one last hoorah for diversifying selection, the authors found a high level of amino acid divergence between the two classes of alleles, thus supporting the maintenance of two functionally distinct protein alleles as a long-term balanced polymorphism (AKA two distinct groups continue to exist).

So what is the take-home message here?  Overall, the authors were able to pinpoint the specific amino acid changes responsible for high altitude hemoglobin adaptation.  The authors confirmed the E7 substitution as responsible for differences in the two gene duplicates, but also revealed a series of mutations, one of particular interest (E13), that are responsible for allelic differences in oxygen affinity between high and low altitude populations of deer mice. Lastly, the authors determined that the distinct alleles are maintained via diversifying selection between high and low elevation populations. Who knows, in the distant future perhaps energy drinks derived from mouse-hemoglobin will allow mountaineers to climb just a bit higher…

The main paper:
Storz, J. F. et al. The molecular basis of high-altitude adaptation in deer mice. PLoS Genet. 3, e45 (2007).

The others:
Snyder LRG (1978) Genetics of hemoglobin in the deer mouse, Peromyscus maniculatus. I. Multiple α- and β-globin structural loci. Genetics 89: 511–530.
Snyder LRG (1978) Genetics of hemoglobin in the deer mouse, Peromyscus maniculatus. II. Multiple alleles at regulatory loci. Genetics 89: 531–550.
Snyder LRG (1980) Closely linked alpha-chain hemoglobin loci in Peromyscus maniculatus and other animals: Speculations on the evolution of duplicate loci. Evolution 34: 1077–1098.
Snyder LRG (1981) Deer mouse hemoglobins: Is there genetic adaptation to high altitude? Bioscience 31: 299–304.
Snyder LRG (1985) Low P50 in deer mice native to high altitude. J Appl Physiol 58: 193–199.
Snyder LRG, Born S, Lechner AJ (1982) Blood oxygen affinity in high- and low-altitude populations of the deer mouse. Respir Physiol 48: 89–105.
Chappell MA, Snyder LRG (1984) Biochemical and physiological correlates of deer mouse α chain hemoglobin polymorphisms. Proc Natl Acad Sci U S A 81: 5484–5488.
Chappell MA, Hayes JP, Snyder LRG (1988) Hemoglobin polymorphisms in deer mice (Peromyscus maniculatus): Physiology of beta-globin variants and alpha-globin recombinants. Evolution 42: 681–688.
Higgs DR, Vickers MA, Wilkie AOM, Pretorius I-M, Jarman AP, et al. (1989) A review of the molecular genetics of the human α-globin gene cluster. Blood 73: 1081–1104.

Second Mouse:
Mighty mouse:

Sunday, March 20, 2011

Adaptation to cold climate in the woolly mammoth

Genetics of Adaptation Graduate Seminar
Author: Elizabeth Brown

Woolly mammoths are iconic animals in North American and Eurasian lore.  Paintings of these amazing animals line caves dating back over 10,000 years, and their ivory has been used to create figurines as long as 35,000 years ago.  Woolly mammoths, now extinct, lived during the last ice age and were well adapted to cold environments.  Some of these adaptive features include small ears and tail, and thick fur covering their body.  Although woolly mammoths displayed these features, because they are extinct one would think investigating the genetic basis of cold adaptation should be impossible.  However, the use of ‘ancient DNA’ has enabled DNA analyses to be performed on mummified tissues and skeletal material dating back up to 1 million years. 

The woolly mammoth belongs to the Elephantid lineage, which includes the African and Asian elephants.  This lineage originated in Africa approximately seven million years ago and is well described.  Woolly mammoths, unlike the African and Asian elephants, moved from a tropical to an Arctic environment, which facilitated possible physiological specializations to cold climates.

One such adaptation to a cold environment is the differential binding and unloading of oxygen, a requirement for many metabolic processes, to locations throughout the body.  Hemoglobin is the protein responsible for such transport. This protein is a four-part molecule located in the blood.  In most mammals the process of oxygen unloading is temperature-dependent, such that small increases in temperature can cause large decreases in the affinity of hemoglobin for oxygen.  This allows for increased oxygen unloading to warmer exercising muscles that have increased metabolic requirements.
In Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance, Campbell et al. explain the methodology used to conclude that the hemoglobin of woolly mammoths possess unique attributes that have enabled them to thrive in cold environments (Nature Genetics 2010).  They first extracted DNA from a 43,000 year old Siberian mammoth specimen.  Despite the obvious advantage of sequencing ancient DNA in the analysis of genes of extinct organisms, this is a very difficult and sensitive process.  It is not uncommon for ancient DNA samples to be degraded and/or contaminated with modern DNA.  So, after careful handling, the DNA sequence of the area encompassing the α-globin and β/δ globin genes, genes coding for any one of four parts of the hemoglobin molecule, was located and then compared to blood samples obtained from both African and Asian elephants. 

The authors found three amino acid substitutions located within the β/δ fusion gene of the woolly mammoth.  A substitution is a type of mutation in which single amino acid is altered.   Two of these mutations occur on the surface of the protein, whereas the last is located at the interface between two of its subunits.  Since each subunit slides and rotates in conjunction with the other parts of the protein, the location of the latter mutation causes extensive conformational modifications to the complex as a whole.
This same mutation is also found in Rush hemoglobin, a mutant human hemoglobin protein.  Since the woolly mammoth is extinct, the true function of this mutation can only be inferred from extant species with similar mutations.  In humans, this mutated protein has been found to cause hemolytic anemia, a disease in which red blood cells are abnormally broken down.  Within the Rush protein, two additional chlorine (Cl-) binding sites are found.  Cl- negatively regulates the affinity of hemoglobin for oxygen, so when more Cl- atoms bind to hemoglobin, the attraction between hemoglobin and oxygen decrease and when fewer Cl- atoms bind, attraction increases.  When higher numbers of Cl- atoms can bind, changes in temperature have a smaller effect on hemoglobin-oxygen affinity.  This would be energetically advantageous in cold-tolerant mammals, ensuring a consistent delivery of oxygen to the extremities, where the temperature of these regions may significantly differ from the core body temperature.

The authors wanted to determine whether the functional characteristics of the human Rush protein are in fact similar to that of the woolly mammoth hemoglobin protein.  To do this, they inserted woolly mammoth-specific substitutions into an Asian elephant hemoglobin protein and then compared it to a protein without the mutations.  Next, they compared the functions of these proteins at multiple temperatures, and striking functional differences were observed.  Interestingly, the woolly mammoth hemoglobin possessed higher oxygen affinity than the Asian elephant hemoglobin at all temperatures tested.  This is shown in the upper figure at 37°C.  In the absence of Cl- atoms, woolly mammoth hemoglobin become saturated with oxygen much sooner than those of the Asian elephant.  This would drastically impair the ability of hemoglobin to distribute oxygen throughout the body.  However, upon the addition of Cl- atoms, there was a significantly reduced effect of temperature compared to that of Asian elephant hemoglobin.  This is shown in the figure below, in which there are substantial differences between proteins without any molecules that alter protein function compared to those that have Cl- or other effector molecules.  These results, in conjunction with those of the Rush protein, confer the adaptive role of this specific substitution for increased cold tolerance.

Campbell et al. also determined that the location of the substitution resulting in increased Cl- binding is very specific.  Changing the mutated amino acid to a structurally different and chemically distinct amino acid all produce radically increased oxygen affinities, however there was no decrease in the effect of temperature, a feature of woolly mammoth hemoglobin.  This demonstrates that the functional properties of the hemoglobin molecule at this location are mediated by the size and specific chemistry of the substituted amino acid.

Since woolly mammoths have been extinct for approximately 10-12,000 years, the true adaptive significance of this single amino acid substitution cannot causally be tested.  However, the physiological innovations that have evolved in the past are of fundamental importance in the study of evolutionary biology and can provide insight on functional traits in both past and present species.

MicroRNAs Contribute to Lake Malawi Cichlid Diversity

Genetics of Adaptation Graduate Seminar
Author: Bethany A. Stahl

Cichlids are an amazingly diverse group of fishes that live in a series of rift lakes in SE Africa.  Rift lakes consistently experience water-level fluctuations that can temporarily form or breakdown isolation barriers of gene flow between adjacent populations.  As a consequence of isolation and rapid changes in the environment, species of cichlids have adapted a suite of unique morphological traits.  Adaptive characteristics can range from a mouth on the side of their head for feeding on scales of other fishes, to specialized jaws and teeth for feeding, and even range in color from blue-striped to black and spotted.  Since hundreds of these morphologically diverse species have evolved from a single common ancestor, they are an excellent model for investigating the genetic consequences of speciation (Loh et al., 2010).   

Though cichlid physical characteristics can vary significantly, their genomes are extremely similar (Moran and Kornfield, 1993; Loh et al., 2008).  Loh et al. (2010) suggested that microRNAs, molecules that “tinker” with the expression of RNA transcripts, may be the root of some of the observed cichild diversity.  The microRNA can act as a light switch to turn genes either on or off, or even a “mood-setting dimmer” to tone down the expression of a gene.  These elements are not part of the gene itself, yet play an important in the expression of physical traits.

Genes are composed of hereditary material termed DNA, and provide instructions for making the proteins that build the physical structures (phenotype) visibly seen in organisms.  Though genes seem to be the basic components leading to phenotype, additional regulatory elements play a role in gene expression.   Transcription factors are proteins that can regulate expression by binding to the enhancer or promoter regions of DNA located adjacent to the genes they regulate.   Similarly, miRNA functions in gene expression by targeting mRNA to repress or silence a gene, but differ from transcription factors in that they regulate genes after transcription has already occurred.

Loh et al. (2010) investigated miRNA as a potential target for phenotypic evolution.  They analyzed numerous cichlid sequences for the target region where the miRNA would normally bind to regulate the gene.  Comparisons were made between cichlids and other fish species.  Over 6,000 miRNA target sites were identified, and within these sites 1,002 SNPs were found.  Loh et al. (2010) further investigated the variation by mapping the substitutions to the physical locations within the genome and found that the predicted sequences fell within the 3’-UTRs – the region immediately downstream of a gene.  To determine the uniqueness of these sites within the 3’-UTRs, the sequences were compared to other fish genomes, which identified 130 sites exclusive to cichlids (Loh et al., 2010).  They also investigated sequences in the predicted miRNA targets across lineages and found that genetic diversity exists between groups of cichlid fishes (Loh et al., 2010).   In conclusion, Loh et al. (2010) described extreme genome similarity among cichlids, yet found numerous mutations among miRNA binding sites.

Though the data presented by Loh et al. (2010) is intriguing, how does it relate to questions of genetic evolution and species diversity?  Cichlids possess a highly similar genome and do not exhibit much variation within their genes, even when compared to zebrafish (Guryev et al., 2006).  Cichlid fishes experienced rapid changes in their aquatic environment, and isolation of populations have lead to a wide variety of morphological traits including color variation, feeding apparati, and breeding behaviors.  Diversity of cichlid traits has likely been accomplished through numerous changes in gene expression, including the action of miRNAs.  Loh et al. (2010) have identified over 100 distinct miRNAs unique to cichlids.  This number is likely to grow with further investigations since this is likely incomplete due to limited cichlid genome resources.  The sequence variation within the miRNA target sites suggests the miRNAs have experienced divergent selection in Lake Malawi cichlid species (Loh et al., 2010).

Loh et al. (2010) also identified one target site that is very similar between cichlids and stickleback fish.  This site is associated with a Hox gene, which is essential for fin-muscle development and regeneration.  Mutations in the miRNA sites related to Hox genes could be a mechanism underlying the observed  morphological variation in cichlid fishes.  Loh et al. (2010) suggests that other genes that may be affiliated with 3’-UTR binding sites and hope their data can help identify more interactions between miRNAs and genes.  

Clearly many complex elements contribute to gene expression and species diversity.  Genetic elements including genes and other regulatory  “switches,” such as miRNAs, contribute to phenotypic diversification.   When a species encounters a new environment, especially in cases when genes are highly conserved, evolution may be marked by alterations of these other regulatory elements to produce novel traits, potentially leading to adaptation.  miRNA diversity could be one of the numerous mechanisms targeted for changes in gene expression leading to a number of morphological features in cichlids.  As our knowledge of microRNAs and other factors contributing to gene expression expands, it will be exciting to see how it will change our perspectives of genetics of adaptation.

Guryev, V. Koudijs, M.J., Berezikov, E., Johnson, S.L., Plasterk, R.H., van Eeden, F.J., and Cuppen, E. 2006.  Genome Research. 16(4): 491-497.
Loh, Y.E.  2008.  Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.  Genome Biology. 9(7): R113.
Loh, Y.E., Yi, S.V., and Streelman, J.T.  2010. Evolution of MicroRNAs and the Diversification of Species. Genome Biology and Evolution. 3: 55-65.
Moran, P. and Kornfield, I.  1993. Retention of ancestral polymorphism in the Mbuna species flock of Lake Malawi. Molecular Biology and Evolution. 10: 1015-1029.
Won, Y.J., Sivasunder, A., Wang, Y., and Hey, J.  2005. On the origin of Lake Malawi cichlid species: a population genetic analysis of divergence. Proceedings of the National Academy of Sciences.  102: 828-837.

Wild Relatives of Rice: Responding to Changes in the Environment by Becoming an Annual

Genetics of Adaptation Graduate Seminar
Author: Kim Thompson

The tasty and productive rice we enjoy today has some wild relatives with big differences. First domesticated approximately 7000 years ago in China, rice is widely planted and also collected from the wild in Asia and Africa. Domesticated rice depends on humans to persist but wild types can grow un-aided in both swampy and seasonally dry areas in Southeastern Asia and India. Michael Grillo and colleagues from Michigan State University (Grillo et al. 2009) used quantitative trait loci (QTL), genetic regions associated with differences between two wild rice species from southeast Asia (Oryza nivara and Oryza rufipogon) to investigate how the rice we grow began its evolutionary trajectory from wild strains as an adaptation to a drier environment. Oryza nivara is an annual rice plant that lives in an environment that becomes dry for part of the year and Oryza rufipogon is a perennial living in an ever-wet environment, similar to the ancestral species (Figure 1).

Figure 1: Diagram of predicted evolution of Oryza nivara and the cultivar, Oryza sativa subspecies indica from an Oryza rufipogon-like ancestor. Blue background represents an ever-wet habitat; orange indicates a seasonally dry habitat. Although the indica cultivar may have arisen from Oryza nivara, introgression from Oryza rufipogon is also likely to have influenced its genetic composition (Li et al. 2007; Sang and Ge 2007). Diagram from Grillo et al. (2009) supporting information.

Researchers crossed Oryza nivara and Oryza rufipogon, creating a hybrid (F1) population. Oryza nivara is self-pollinated so individuals have less variation at each gene but Oryza rufipogon has high heterozygosity or genetic variability. Therefore two individuals that captured the most genetic diversity present in Oryza rufipogon were selected from the F1, self-pollinated, and grown for two years in a greenhouse, producing two F2 populations (labeled A and B). A total of four populations could then be compared: Oryza nivara, Oryza rufipogon, F2 (A) and F2 (B).

Figure 2: Physical differences between Oryza nivara and Oryza rufipogon rice plants grown under the same greenhouse conditions. (A) Oryza rufipogon has longer stems and more branching (tillering) (B) Oryza nivara has a more compact structure (C) Open flowering structure of Oryza rufipogon. (D) Compact flowering structure of Oryza nivara (figure from Grillo et al. 2009.

Differences in how fertilization occurs (mating system) and the timing of the flowering seasons relative to the amount of daylight they experience (photoperiod sensitivity) contribute to the success of a plant as either an annual or perennial. Therefore, features associated with these differences were measured in this study including: days to flowering after germination, sizes and positions of flowering parts (tiller length, anther length, panicle exsertion and shape, and spikelet number) and grain weight. Each of these is a quantitative trait resulting from the combined effects of multiple genetic and environmental factors, and significant differences are observed between the two study species (Figure 2). In order to measure the genetic differences, simple sequence repeats (SSRs), or microsatellites were used to detect differences among individuals and identify individuals for generating the F2 populations. Differences in SSRs between the species also helped the researchers detect QTL, sets of genes located together on a region of the chromosome and linked to a phenotype (Figure 3).
Figure 3: a) Two different parents (the Oryza species in  this study) differ in a phenotype and become more divergent as they are inbred (self-pollinated) over many generations. b) The parental lines are crossed, providing different genetic and phenotypic combinations in the offspring. These traits can be measured and linked to genetic markers such as SSRs.  c) The probability that a known marker is associated with a QTL is evaluated using statistical techniques to map the QTL on a chromosome and measure how strong is its effect on a particular phenotype. From Miles and Wayne (2008).

Figure 4: Chromosomes 1 and 6 of Oryza rufipogon with select QTL (quantitative trait loci) pictured (abbreviations defined above). Red and blue symbols indicate two different sets of Oryza rufipogon plants that vary in physical and genetic characteristics. Black symbols indicate a combined analysis of the Oryza rufipogon plants. The gene, Hd1 is located near DF6 on chromosome 6 (Grillo et al. 2009).

QTL that affect sizes of flower structures, days to flowering from germination, and length of flowering time were identified in the two wild rice species, Oryza nivara and Oryza rufipogon and in hybrids of the two. The QTL contain genes that are at least partly responsible for those changes (Figure 4). The largest effect observed in the QTL was for timing of flowering (photoperiod sensitivity) so this became the focus of the remainder of the investigation.

 Near a QTL named DF6, scientists know that one gene, Hd1is associated with photoperiod sensitivity. This gene was sequenced from each of the original parents, Oryza nivara and Oryza rufipogon. A mutation in Hd1 was found in the annual rice Oryza nivara, which is photoperiod insensitive. An insertion into the first exon of the gene is thought to have interrupted the proper functioning of the gene so that Oryza nivara is no longer responsive to day-length changes and it continues flowering throughout its life. All second generation hybrids of the two plants (F2 population), were both perennial and sensitive to daily increases in light amount, suggesting that genes for these traits are dominant and that multiple genes are interacting.
If Hd1 is responsible for photoperiod sensitivity, then the original form of the gene, selected from Oryza rufipogon, when inserted into Oryza nivara should make it sensitive to changes in light conditions. However when such transgenic rice plants were developed and grown in long day conditions, they continued to flower, overlapping the normal flowering times of Oryza nivara. This was unexpected since Oryza rufipogon only flowers in short-days and the gene was expected to introduce this sensitivity to the transformed Oryza nivara. This type of transformation was observed in previous studies when the gene was introduced in cultivated rice varieties. Two other genes are suspected to be involved, acting in concert with Hd1 to create the lack of day-length sensitivity that is seen in Oryza nivara.

 How did rice evolve into an annual crop that eventually was domesticated? Some changes may have occurred as it was colonizing a new environment that was drier than that of its ancestors or as a result of ancient climate changes. In order to be successful as an annual plant, rice would need to flower longer and produce an abundance of seeds before it died. Oryza nivara plants start to flower in the middle of the monsoon season, within four months after its seeds germinate, speeding its ability to produce new seeds before the ground dries up. A perennial ancestor would have put more energy into growing stems that persisted after flowering was finished. Its ancestor resembled Oryza rufipogon, which does not flower until the days grow shorter, at the end of the monsoons but which continues growing for many years in the swamps. The loss of sensitivity to seasonal light changes was important for Oryza nivara’s success in a dry environment, allowing it to produce numerous seeds before the rest of the plant perished. This study showed that loss of photoperiod sensitivity is a major factor in evolution from a perennial to an annual plant but that multiple genes interact to create this new phenotype.


Grillo, M. A., C. Li., A. M. Fowlkes, R. M. Briggeman, A. Zhou, D. W. Schemske and T. Sang.  2009. Genetic architecture for the adaptive origin of annual wild rice, Oryza nivara. Evolution 63: 870–883.

Li, C. B., A. L. Zhou and T. Sang. 2006. Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytologist 170:185–194.

Miles, C. and Wayne, M. 2008. Quantitative trait locus (QTL) analysis. Nature Education 1:1.

Sang, T. and S. Ge. 2007. The puzzle of rice domestication. Journal of Integrative Plant Biology 49:760–768.

Vaughan, D. A., B. Lu and N. Tomooka. 2008. The evolving story of rice evolution. Plant Science 174:394–408.

Belugas and Llamas: Living in Thin Air

Genetics of Adaptation Graduate Seminar
Author: Sunita Yadav

One normally does not think of llamas and beluga whales in the same sentence; they look very different and one lives in the ocean whereas the other in the Andes Mountains. Nonetheless, they have adapted to low-oxygen environments in much the same fashion. Llamas belong to the camel family and are divided into 4 species, llama, alpaca, guanaco, and vicuña, all in the genusLama. They live at altitudes above 5000 feet where atmospheric pressure is lower and therefore less available oxygen. The Beluga Whale, Delphinapterus leucas, is ghostly white with a circumpolar distribution in frigid waters around the Arctic Sea. It is one of two members in the toothed order Monodontidae, the other species being the Narwhal. Beluga whales have been known to dive to depths of 500 m, also an oxygen deficient (hypoxic) habitat, and for periods that can exceed 15 minutes at a time in a dive. A third type of hypoxic habitat would be underground environments inhabited by mole rats. The work to date reflects that there are multiple mechanisms that underlie various physiological responses to hypoxic environments.
Mammals employ different physiological adaptations to survive in low-oxygen environments such as: high oxygen affinity to hemoglobin (the respiratory pigment), a reduced heart rate, a lower metabolic rate, a higher blood volume percentage, higher myoglobin content (a protein that stores oxygen in muscle tissue and allows muscle tissue to be active for prolonged periods), and altered distribution of blood flow to tissues.
A first question to ask is why there is less oxygen in deep oceans and high mountains. With increasing altitude, atmospheric pressure is lower resulting in what is generally called ‘thin air’. Basically this means there are less oxygen molecules available per unit of air. In contrast, oxygen in oceans is incorporated by surficial mixing; deep ocean water simply does not mix at the surface very often and therefore is hypoxic. When mammals are exposed to such habitats, their normal oxygen transport does not work well (the reason why we hyperventilate when mountain climbing).
So what happens when a beluga whale dives? If it were not adapted to its deep sea lifestyle, at some point during the dive, the amount of carbon dioxide (CO2) in it’s blood would increase leading to lower pH, reduced oxygen binding in blood (due to reduced oxygen binding to hemoglobin) and probable death because of oxygen starvation. Since beluga whales are not extinct, they have found a way to survive during their deep diving. The question is how?
Under normal pressures, most mammals in a resting state have excess oxygen releasing only about 25% oxygen to tissues. Under active conditions when cells need more oxygen, hemoglobin quickly unloads oxygen to the active cells. Typically, an oxygen disassociation curve is used to describe percent saturation of hemoglobin with oxygen at different atmospheric pressures. Since one hemoglobin molecule can attach 4 oxygen molecules, a 50% saturation (referred to as p50) value is commonly used for comparison. Temperature, pH and other organic molecules affect how quickly an individual reaches the p50 value.
Since belugas and llamas have been living in hypoxic environments for thousands of years, their bodies have adapted to efficiently use lower oxygen amounts. One way they accomplish this is to modulate blood chemistry to make oxygen more attracted to the hemoglobin molecule (this would be a left shift on the oxygen dissociation curve depicted above).
The balance of CO2 and oxygen maintains blood pH. At low pH, hemoglobin has lower affinity for oxygen(curve shifts to the right) whereas at higher pH, hemoglobin has a higher affinity for oxygen (curve shifts to the left). An increase in COreduces pH and restricts binding of oxygen to hemoglobin. Reduced pH occurs because CO2 is converted to carbonic acid by a group of enzymes known as carbonic anhydrases (CA). They form carbonic acid from COat different rates. One form of the CA enzymes is CA II which is 10x to 100x faster than CA I or CA III in forming carbonic acid. The hypothesis is that mammals (like the beluga) living in hypoxic environments would show reduced levels of CA II to maintain pH balance in blood thereby maintaining high oxygen attraction for hemoglobin.
By comparing the expression levels (quantities) of CAs in different species, researchers have begun to explain the underlying physiological adaptations that beluga whales and other mammals employ. One research group (H. Yang and colleagues) used blood samples from the dromedary camel, domestic llamas, and beluga whales to separate and quantify CAs. Remember that CA II was the fastest in converting CO2 to carbonic acid; not good if you are a beluga whale or llama. Well, what did they find? CA II was not detected in red cells of beluga whales and reduced levels were found in llamas. Camels though closely related to llamas displayed a typical mammalian ratio with greater CA I levels in relation to CA II. In studies of mole rats (underground lifestyle), CA II was also deficient in red blood cells.
Storz and colleagues used deer mice (Peromyscus maniculatus) that live at different elevations to study adaptation to altitude. Genetic studies comparing mice populations at various elevation zones revealed differences in allelic forms (version of a gene) of α and β globin genes (type of protein) that code for hemoglobin structure. Mice that live at higher elevations show a higher prevalence of the genetic code for the version of the gene that ultimately leads to a destabilized hemoglobin molecule. What does this mean? An unstable hemoglobin molecule shows a higher attraction for oxygen. Mice in lowlands had a different β –globin (more stable hemoglobin) than mice in highlands (unstable hemoglobin, i.e. higher affinity to oxygen). This implies some sort of divergent selection based on habitat locations of deer mice.
More recent work on humans living on the Tibetan plateau by Xan Yi and colleagues shows a strong positive selection on a different pathway. Exomes (coding regions in the DNA) of 50 Tibetan individuals were sequenced. Differences were found at a single location (single nucleotide polymorphism or SNP) on the genome for a gene called EPAS1 between highland Tibetan and lowland Han populations. EPAS1 is a transcription factor gene involved in hemoglobin concentration in red blood cells. Most humans react to low oxygen levels by producing more hemoglobin which can make blood more viscous (and also lead to altitude sickness), Tibetans, however, have relatively low hemoglobin concentrations. Therefore, Tibetans avoid the symptoms of altitude sickness. How they actually get enough oxygen is yet to be decoded. If you have ever wondered why Ethiopian and Kenyan athletes frequently win marathons, you will not be surprised to learn that the runners all come from highland areas in those countries. Their adaptation to high altitude allows them to use oxygen more efficiently.
Researchers are also actively studying different species such as, plateau pika, mountain sheep, and orca whales to study variation in adaptation to hypoxic habitats across species. The earlier studies in llamas and beluga whales have not been repeated to verify DNA sequence level differences in gene expression (amount of a gene that is produced to make a certain number of protein molecules) or regulation (whether a gene is activated or not). Thus far, the research in llamas, belugas, deer mice, and humans suggests that there are multiple pathways for adaptation to low oxygen habitats.
Storz, J.F., Runck, A.M., Sabatino, S.J., Kelly, J.K., Ferrand, N., Moriyama, H., Weber, R.E. and A. Fago, 2009, Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin, PNAS, Vol. 106(34): 14450-14455.
Yang, H., Hewett-Emmett,D. and Richard E. Tashian, 2000, Absence or Reduction of Carbonic Anhydrase II in the Red Cells of the Beluga Whale and Llama: Implications for Adaptation to Hypoxia, Biochemical Genetics, Vol. 38(7/8):241-252.
Yi, Xan et al., 2010, Science, Vol. 329(5987): 75-78.

Searching for the genetic basis of adaptation in Bees

Genetics of Adaptation Graduate Seminar
Author: Priya Date

It is a common view among scientists who study human evolution that humans originated on the African continent and then migrated. Isn’t it surprising how different people from different parts of the world look? Not only do we look different, but also we can have very different styles of living. One important question is, if these differences are culturally transmitted, or genetically heritable, i.e., we pass them down to our kids through our genes (DNA). However, because of our long life spans, late age of reproduction and difficulty to conduct genetic experiments in humans, it is very difficult to study these kinds of questions. This is when other organisms like the little buzzing critter ‘the honey bee’ can come to our rescue.

The honeybees also originated in Africa and have then expanded in range to Asia and Europe due to introduction by humans. These bees are thus now living in different parts of the planet (thanks to us !) and show region-specific adaptations in how they look or behave. Bees in Europe that had genes that helped them to survive in the cold climate reproduced and thus passed on the heritable component of their DNA for cold survival to the next generation. The same is true for why the bees from Europe look different from the African bees. Even though we have some indication that some genes are involved in adapting to new environments, we still don’t know what regions of the whole genome of any organism are important for these adaptations. In this study by Zayed and Whitfield (PNAS article, 2008) scientists have taken the opportunity to take advantage of the sequenced genome of honeybees to look for signature of selection. By signature of selection we mean whether changes in certain parts of the genome are increasing in frequency in the population in a geographic location specific manner. This would then indicate that those genomic regions have some adaptive value to increase the bee’s fitness or survival in any given environment.

Before we delve into the details of this study lets take a few moments to refresh our basics of molecular biology. The genome of any organism is a huge string of DNA. The DNA sequence is made up of four bases which are read as A, T, G and C. As we make words by putting together certain alphabets in the right sequence, the DNA sequence when put in the right order makes genes, which encode proteins. And just like changing the sequence of alphabets in a word will make it meaningless, changing the sequence of DNA makes different proteins that might be non-sense proteins. Very rarely, these changed or damaged proteins in turn may result in changing how we look or behave. We only store the changes that are beneficial and generally get rid of those which are harmful. However, genes form only a small proportion of the whole genome, sometimes as little as 1% in certain organisms: much of it may code for nothing but is important for regulating the expression of the coding region. However, in this study the authors focus on only the coding regions. Thus if we want to find out if certain regions of the genome have changed to suit the environmental needs we can compare the ancestral genome with the derived or newer genome and screen for signatures of selection.

Zayed and Whitfield have compared certain genomic regions of the African, Asian, East and West European bees for changes in the DNA sequence. To do such comparison researchers have developed very complicated statistic called ‘Fst’. In simple words, it goes from 0 to 1 where 0 indicates no genetic differences between if two DNA sequences and 1 indicate a lot of differences in the DNA. Thus, if the derived genome were to be very similar to the ancestral genome its Fst would be 0 and if it were diverged the Fst would be 1. In the bee study, the authors found that the West European population of bees was significantly diverged from its ancestral African population, but the other two populations, however, do not show any evidence for divergence at this stage (Figure 1). This may be due to the fact that the Asian and East European environment is somewhat similar to the African environment. This data suggest that the vast differences seen in the West European and African bees has a strong genetic basis and more functional studies relating the two should be performed. 

Finally, turning back to the questions we started with to understand how the we look different, studies like this can provide some common rules or generic principles which will hold true anywhere. As the bees, which originated on the African continent when moved to the colder climate of West Europe changed in order to survive in the new environment, humans have also evolved several adaptations. For example, a study shows genome-wide signatures of selection acting on certain pigment related genes in Asian, European and African people (Genetics-of-human-pigmentation). This can be explained as the people inhabiting the tropical regions have darker skin pigment to gain protection from the uv radiation and thus have diverged in skin color from their European counterparts. Not only skin color but several such examples leading to difference in our height, stature, behavior, etc. can be found which probably have similar genetics and animal models like the honey bees can be used to understand these genetic mechanisms.