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Finch character displacement

Posted in Epigenetics and Environmental Factors, Gene Regulation and Evolution, Genome Biology, tagged beak size, Darwin's Finch's, Darwinian evolution, Galápagos Islands on April 23, 2016| Leave a Comment »

Finch character displacement

Larry H. Bernstein, MD, FCAP

LPBI

Genetic Study of Darwin’s Finches Catches Evolution in Action

http://www.genengnews.com/gen-news-highlights/genetic-study-of-darwin-s-finches-catches-evolution-in-action/81252647/

http://www.genengnews.com/Media/images/GENHighlight/Apr22_2016_PeterRGrant_MediumGroundFinch2037196235.jpg

The medium ground finch (Geospiza fortis), shown here, diverged in beak size from the large ground finch (Geospiza magnirostris) on Daphne Major Island, Galápagos following a severe drought. Genomic screening of the genomes of medium ground finches revealed that a particular gene, HMGA2, played a large role in the rapid evolution of a smaller overall beak size in the medium ground finch. [Peter R. Grant]

An evolutionary phenomenon first described by Charles Darwin has the support of new and unusually strong supporting evidence. The phenomenon, called character displacement, may occur when species compete for the same food source. The species may evolve different body shapes, such as different beak sizes in the case of finches, diverging from each other until they relieve competitive stress.

Darwin developed the idea of character displacement after observing the finches of the Galápagos Islands. He proposed that changes in the size and form of the beak have enabled different species to utilize different food resources, such as insects, seeds, and nectar from cactus flowers, as well as blood from seabirds.

In a study of character displacement among Darwin’s finches, researchers from Uppsala University and Princeton University have now identified a gene that explains variation in beak size within and among species. The gene contributed to a rapid shift in beak size of the medium ground finch following a severe drought.

The details of the study appeared April 22 in the journal Science, in an article entitled, “A Beak Size Locus in Darwin’s Finches Facilitated Character Displacement during a Drought.” The article describes how the researchers alighted on a gene called HMGA2 after screening the genomes of medium ground finches that survived or died during a drought that occurred between 2004 and 2005. The researchers found that the HMGA2 gene comes in two forms: one is common in finches with small beaks, whereas the other is common in finches with large beaks. The proportion of the two forms in the birds’ genome changed as a result of the better survival of birds with small beaks.

“We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin’s finches on Daphne Major in the Galápagos Islands,” wrote the authors. “We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin’s finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event.”

In a previous study from the same team, the ALX1 gene was revealed to control beak shape (pointed or blunt). The HMGA gene that figures in the current study was previously associated with variation in body size in dogs and horses, and it is one of the genes that show the most consistent association with variation in stature in humans, a trait that is affected by hundreds of genes. HMGA2 has also a role in cancer biology as it affects the epithelial–mesenchymal transition (EMT) that is important for metastasis and cancer progression.

“Our data show that beak morphology is affected by many genes, as is the case for most biological traits,” said Sangeet Lamichhaney, the current study’s first author and a doctoral student in the laboratory of Leif Andersson, one of the study’s senior authors and a genomics professor at Uppsala. “However, we are convinced that we now have identified the two loci with the largest individual effects that have shaped the evolution of beak morphology among the Darwin’s finches.”

Andersson collaborated with Princeton researchers Peter Grant, the Class of 1877 Professor of Zoology, Emeritus, and B. Rosemary Grant, a senior research biologist, emeritus, in ecology and evolutionary biology.

“It was an exceptionally strong natural-selection event,” noted Peter Grant, who pointed out that that because Daphne Major is in an entirely natural state, the occurrence was completely unaffected by humans. “Now we have demonstrated that HMGA2 played a critical role in this evolutionary shift and that the natural selection acting on this gene during the drought is one of the highest yet recorded in nature.”

“This research tells us that a complex trait such as beak size can evolve significantly in a short time when the environment is stressful,” Rosemary Grant added. “We know that bacteria can evolve very quickly in the lab, but it is quite unusual to find a strong evolutionary change in a short time in a vertebrate animal.”

Linked loci and Galapagos finch size

Observations of parallel evolution in the finches of the Galapagos, including body and beak size, contributed to Darwin’s theories. Lamichhaney et al. carried out whole-genome sequencing of 60 Darwin’s finches. These included small, medium, and large ground finches as well as small, medium, and large tree finches. A genomic region containing the HMGA2 gene correlated strongly with beak size across different species. This locus appears to have played a role in beak diversification throughout the radiation of Darwin’s finches.

Science, this issue p. 470

Ecological character displacement is a process of morphological divergence that reduces competition for limited resources. We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin’s finches on Daphne Major in the Galápagos Islands: The medium ground finch diverged from its competitor, the large ground finch, during a severe drought. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin’s finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event: Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59). Thus, a major locus has apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin’s finches.

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Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

Posted in Biological Networks, Gene Regulation and Evolution, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Genome Biology, Interviews with Scientific Leaders, Medical and Population Genetics, Population Health Management, Genetics & Pharmaceutical, Proteomics, Statistical Methods for Research Evaluation, tagged Darwin, Darwinism, Evolution, food, Galápagos Islands, Marcus Feldman, Natural selection, Organism, Protein folding, Stanford on March 16, 2013| 4 Comments »

Article 2.5: Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

Reporter: Aviva Lev-Ari, PhD, RN

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UPDATED 9/16/2013

VIDEO CLIPS

Enzymes That Are Not Proteins: The Discovery of Ribozymes

Listen to past HHMI President Dr. Thomas Cech discussing his Nobel Prize-winning discovery of RNA’s catalytic properties.

http://www.hhmi.org/biointeractive/enzymes-are-not-proteins-discovery-ribozymes

Stanford Report, March 15, 2013

Long-term evolution is ‘surprisingly predictable,’ Stanford experiment shows

A protein-folding simulation shows that the debated theory of long-term evolution is not only possible, but that the outcomes are predictable. The Stanford experiment provides a framework for testing evolutionary outcomes in living organisms.

BY BJORN CAREY

L.A. Cicero

Visiting scholar Mike Palmer left, and Professor Marcus Feldman

Dr. Michael Palmer, left, and Professor Marcus Feldman, with co-author Arnav Moudgil (not pictured), found that the long-term evolutionary dynamics were surprisingly predictable in a model of protein folding and binding.

Two birds are vying for food. One bird’s beak is shaped, by virtue of a random mutation, such that it’s slightly more adept at cracking seeds. This sets the bird on the road toward acquiring more food, a better chance of scoring a mate and, most important, passing on its genetic endowment.

This individual’s success is an example of short-term evolution, the widely accepted Darwinian process of natural selection by which individual organisms that have better adapted to their surroundings prevail.

In recent years, however, some scientists have argued that natural selection occurs not just at the individual organism level, but also between lineages over the course of many generations. In a new study, Stanford biologists have demonstrated that not only is this long-term evolution possible, but that long-term evolutionary outcomes can be surprisingly predictable.

The group set up a computer simulation in which 128 lineages of proteins continuously folded into new shapes, competing to bind with other molecules, called ligands, in each new configuration. The better each protein could attach itself to the ligands, the more ligands it would scoop up, and the higher its fitness – that is, its average number of “offspring” – would be. The simulation was run for 10,000 generations.

Although the chaos of 128 lineages – a total of more than 16,000 individual proteins – mutating over thousands of generations might seem unpredictable, and that it would be nearly impossible for the same thing to happen twice, it’s actually the opposite.

“Even though things look complicated, the possible evolutionary trajectories are quite constrained,” said lead author Michael Palmer, a computational biologist at Stanford. “There are only a few viable mutations at any point, which makes the dynamics predictable and repeatable, even over the long term.”

The study, co-authored by Marcus Feldman, a biology professor at Stanford, and Stanford research biologist Arnav Moudgil, was recently published in the Journal of the Royal Society Interface.

In some experiments, the lineages that consistently came out on top in the long term were not initially the best adapted at binding to ligands. “The immediate fitness is not the only important thing,” Palmer said. “Yes, a lineage does have to survive in the short term. But just as important is how it is able to adapt to new and potentially variable environments over the longer term.”

A good example of this scenario is Darwin’s famous finches. It’s thought that individuals – perhaps just a single pair of birds – from a South American species ended up on the Galápagos Islands about 1 million years ago. Today their descendants have diversified into about 15 modern species. Some eat seeds, some eat insects, or flowers. Some eat ticks, or even drink the blood of other birds.

“If there was some catastrophe that removed one of those food sources, it might wipe out one or more of the 15 species, but the rest of the lineage – the descendants of that initial pair of birds – would persist,” Palmer said. “Now say there was a competing lineage that was great at cracking seeds, but unable to evolve to other diets due to some prior genetic constraint. The same catastrophe could wipe it out.”

The finding, and others like it, could represent a significant shift in viewpoint for biologists. For one thing, it means that in certain situations, scientists should look beyond the details at the level of the individual organism, as the evolutionary dynamics can be accurately understood as lineage selection.

It also has implications on a species’ genomic architecture, or how a genome is organized on the lineage level. While a lineage’s genome might primarily select for a particular set of traits in order for individuals to survive in the short term, in order to out-compete other lineages, it must also be able to adapt to new conditions over the long term.

“An individual can have a lucky mutation that produces an immediate adaptation,” said Palmer. “Or a lineage can have a lucky mutation that happens to position it to adapt to the range of environments it will experience over the next thousand generations. A single mutation can have a distinct short-term and long-term fitness.”

The authors believe that the work can be replicated in microorganisms, and are now hoping that microbiologists will apply the new metrics of selection in vitro.

“There is already some evidence in vitro that there is a lot of constraint on evolutionary trajectories,” Palmer said, “and we think we’ve come up with a good framework to quantify evolutionary predictability and long-term fitness.”