Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

Weedon et al. concluded that the HMGA2 gene was one of several that has a role in influencing height in adult humans.

Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions.

When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result is dwarfism. This protein is associated with the HMGA2 gene.

Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 – 300,000 years ago.

Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed simply showed no correlation whereas other factors showed a correlation with beak size, but not beak shape.

However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. magnirostris. This divergence happened on an isolated Galapagos island 22 years after G. magnirostris arrived to share a habitat with G. fortis.

Thanks to the long-term scientific field work of Peter and Rosemary Grant, scientists have developed an understanding of how this speciation has happened.

Jonathan Weiner provides an introduction to this legendary fieldwork in The Beak of the Finch.

For a more scholarly background, check out How and Why Species Multiply by Peter and Rosemary Grant.

Coupled with the team's previous study that showed the ALX1 gene controlled beak shape, this study shows evidence that HMGA2 is associated with beak size.

These findings show how scientific research builds upon itself to continue to not only answer questions, but to continue to ask questions.

Movement of genes from one species into the gene pool of another species by the repeated crossing of a hybrid with one of its parents.

To look at the specific finches that experienced the 2004–2005 drought, the researchers genotyped a HMGA2-specific SNP in both survivors and victims (71 total birds).

Lamichhaney and colleagues took a closer look at another 133 birds. Specifically, they investigated an SNP at a certain position in the genome.

Within the 17 SNPs, researchers knew that the large finches were homozygous (LL in Figure 2D) for one haplotype group and small finches were homozygous (SS) for another haplotype group. However, what was going on with the medium ground/tree finches?

This particular SNP was shown to be associated with only beak and body size within these medium finches.

HMGA2 had been identified as a candidate gene, and the SNPs within the 525-kb region within HMGA2 had been located. Therefore, the researchers attempted to see which trait this gene was specifically related to.

In contrast to haplotypes present in large and small finches, the medium-sized finches tended to inherit the particular genes from both parents.

This is what we may call a heterozygous condition.

Researchers performed pairwise, genome-wide fixation index (see definition in Glossary section) scans across the whole genome. They did this with 15kb windows that were non-overlapping regions.

The following three comparisons were made: 1) large ground/tree versus medium ground/tree; 2) large ground/tree versus small ground/tree; and 3) medium ground/tree versus small ground/tree.

A compilation of SNP calls yielded 44,767,199 variable sites within or between populations. The fixation index score ranged from zero (complete sharing of genetic material) to one (no sharing of genetic material).

Each index value was then transformed into a Z-score, which is simply a measure of how many standard deviations below or above the population mean a raw score is. Further analysis was done if the Z-score of the fixation index was greater than five. See the Supplementary Materials for more information.

The researchers again calculated the fixation index. However, this time it was only for the variable region (~525-kb in size) that contained the HMGA2 gene.

Remember, the fixation index score ranged from zero (complete sharing of genetic material) to one (no sharing of genetic material).

For a good explanation of a SNP, see this video.

Where a single nucleotide base is changed, which results in a different amino acid.

Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features, such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

Ligon et al. (2005) had previously reported an 8-year-old boy with a shortened HMGA2 gene that exhibited widely-spaced eyes, a large head circumference, and premature dentition.

Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions. When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result is dwarfism. This protein is associated with the HMGA2 gene.

The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 — 300,000 years ago.

Hybridization in finches has influenced the evolution of beak shape. Using phylogenetic studies along with genomic data allowed researchers to reveal some of the genetic variation that underlies finch beak diversity.

DNA extraction and whole genome sequencing was performed using samples from 60 birds. In addition, 120 bird samples from a previous study (Lamichhaney 2015) were used.

The sequence reads were analyzed and trimmed using FASTQC software and FASTX software, respectively. To see more specific software used, see the Supplementary Materials

The researchers used the genome assembly of a medium ground finch as a reference genome. The reads from the samples were aligned to this reference.

Lamichhaney et al. (2015) previously scanned the genomes of finch populations that were related but displayed different beak structures. They found that the ALX1 gene was a strong candidate for regulating the variation in beak morphology. ALX1 encodes a protein that is vital in developing structures from embryonic tissue that will form craniofacial structures.

Grant and Grant (1994) explored hybridization among finch species over 17 years. They concluded that hybrid traits were morphologically intermediate, which indicated the parent genes contributed to the offspring phenotype equally. Hybrids also varied more phenotypically.

Even though both were heritable, beak size seemed to be more important that body size because the beak's relationship to food acquisition.

The 2004–2005 selection event was a severe drought. For a thorough explanation of the climate of the Galapagos islands, see here.

Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. magnirostris. This divergence happened on an isolated Galapagos island 22 years after G. magnirostris arrived to share a habitat with G. fortis.

After the drought, medium ground finches with larger beaks were at a severe disadvantage because they could not compete for food with the large ground finches.

When a genotype is shown to be disadvantaged, what happens to the genes in that gene pool? What happens to those disadvantaged individuals? What happens to the population as a whole?

Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed no correlation whereas other factors showed a correlation with beak size, but not beak shape. However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

This index scan allowed the researchers to narrow down the region that showed the strongest differences between the large, medium, and small ground and tree finches.

The investigators were able to rule out the six other loci that may have been associated with beak size, body size, or beak shape.

Investigations within the HMGA2 gene showed that it did, in fact, show a high relationship with beak size.

This seems to confirm the fact that HMGA2 played an important role in the evolutionary shift in beak size during the drought.

Introgression, the movement of a gene from one species into the gene pool of another, has been known to speed up a population's response to an evolutionary selective pressure. It does this by increasing genetic diversity.

Grant and Grant documented recurring introgressive hybridization between medium ground finches and small ground finches.

Introgression, the movement of a gene from one species into the gene pool of another, has been known to speed up a population's response to an evolutionary selective pressure. It does this by increasing genetic diversity.

Grant and Grant documented recurring introgressive hybridization between medium ground finches and small ground finches.

Brown and Wilson (1956) argued that character displacement was a common part of geographical speciation. They explained that displacement happened most often as a product of genetic and ecological interaction when species first met.

Grant and Grant (1994) explored hybridization among finch species over 17 years. They concluded that hybrid traits were morphologically intermediate, which indicated the parent genes contributed to the offspring phenotype equally. Hybrids also varied more phenotypically.

This single HMGA2 locus seems to allow for diversity among finch beak size. However, the exact mechanism for how HMGA2 controls beak size in finches is unknown.

Would the findings of this study provide enough justification for further studies that would attempt to better understand that function of HMGA2?

The HMGA2 gene is strongly associated with beak size. Beak size is the main factor that allowed some medium ground and tree finches to survive after a drought.

Thus, the researchers provided a direct link between this particular gene and the fitness of finches.

Why was it important to not only construct a phylogenetic tree based on the entire genome sequences (Fig. 1C), but also construct one based on the HMGA2 region (Fig. 1D)?

What do these two trees reveal about the differing sizes of finches?

For the first time, researchers have been able to find a gene that controls beak size in Darwin's finches. Why is this finding such an important part of the story of these birds and how they evolved?

In addition to Darwin's finches, this story about lizards provides another great example.

Jonathan Losos also wrote a popular book, Improbable Destinies: Fate, Chance, and the Future of Evolution, that highlights these anole lizards.

The investigators initially had to decide that they were going to use samples from six species of finches. Then, they screened the entire genome of these species to look for genetic variants in different individuals. The objective was to see if any variation at any given location was associated with size and/or size-related traits.

The genome-wide fixation index scan found that a region around 525 kb in size showed the most striking differences.

Lamichhaney and colleagues constructed another phylogenetic tree based on the alignment of this region in all of the samples.

The nucleotide alignment of the variable positions from all 180 samples (60 birds plus 120 from previous study) allowed the scientists to generate a phylogeny using software FastTree.

See here to learn more about FastTree and its maximum-likelihood method.

Lamichhaney and colleagues sequenced a total of 60 birds. Sequencing is a technique used to actually read the DNA.

For a history of DNA sequencing and assembly, this resource from HHMI BioInteractive is a great tool.

This video shows specifically how Illumina Sequencing Technology works.

If a finch genome is 1 Gbp (one trillion base pairs), sequencing "to ~10x coverage per individual" would mean that you obtain 10 Gbp of sequencing data.

"Using 2 x 125-base pair paired-end reads" refers to the fact that the fragments sequenced were sequenced from both ends and not just one. Refer to the videos above for more information.

Genotyping establishes a genetic code for each individual finch. With birds, this can typically be done using plucked feathers, blood, or eggshell membranes.

The researchers here used blood samples that were collected on FTA paper and then stored at -80°C. FTA paper is treated to bind and protect nucleic acids from degrading.

This type of scanning is used to identify specific gene markers that are highly variable. Researchers wanted to identify a locus that showed beak size variation.

HMGA2 is a gene that plays a role in transcribing HMGA proteins. These proteins are associated with chromatin, the substance that makes up chromosomes and can consist of DNA, RNA, and proteins.

Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

Stuart and Losos (2013) found that just over 6% of the cases they reviewed that highlighted character displacement actually showed strong examples. However, one study not only documented ecological character displacement, but also showed it happening in real time. This was the long-term experiment of Darwin's finches by Grant and Grant (2006).

Darwin states in The Origin of Species that the differences between species is caused by divergence. It is this divergence that acts to minimize the competitive interactions between similar populations.

Brown and Wilson (1956) later argued that this concept (they called it character displacement) was a common part of geographical speciation. They explained that displacement happened most often as a product of genetic and ecological interaction when species first met.

Referring to traits that are controlled by two or more genes at different places on different chromosomes.

When two or more genomic regions are derived from a single ancestor.

Type of natural selection where one phenotype is favored over others. This causes the frequency of alleles to shift in the direction of that phenotype.

An individual that has two different forms of a particular gene on homologous chromosomes.

Referring to a particular gene in which all of the alternative forms of that gene are identical on homologous chromosomes.

Observable characteristics of an individual.

Refers to a variation in a single base pair within a DNA sequence.

An essential copying of DNA into RNA, the first step of gene expression.

Measure of the genetic differences in and among populations due to genetic structure.

Measures the difference between the average genetic value of selected organisms and the average genetic value of all the organisms in the population.

Used to explain the relationship between a dependent variable and one or more independent variables.

Referring to traits that are transmissible from parent to offspring.

Groups of one or more populations.

Referring to the study of the evolutionary history and relationships of various biological species.

The formation of new species.

Groups of genes inherited from a single parent.

The process of measuring or comparing features such as DNA sequences, variation of structures, gene functions, or gene expression.

Event in which a lineage rapidly diversifies into more species with different adaptations. These events lead to speciation.

Relating to the structure or form of living organisms.

When two competing species overlap in habitat, natural selection may drive one population to use resources that are not used by individuals of the other population. This allows two similar species to coexist.

Describing a branch of biology that deals with relationships and interactions among organisms and the environment.

Referring to the study of the evolutionary history and relationships of various biological species.

Relating to the structure or form of living organisms.

Individuals of different species compete for the same resources.

Events in which a lineage rapidly diversifies into more species with different adaptations. These events lead to speciation.

The formation of new species.

A statistic that describes how much variation of a specific trait can be attributed to genetics. With these finches, it's a measure of how well differences in beak genes account for differences in beak sizes.

Process that describes how species adapt to their environment. The organisms that are best adapted tend to survive and reproduce.

Describing a branch of biology that deals with relationships and interactions among organisms and the environment.

When two competing species overlap in habitat, natural selection may drive one population to use resources that are not used by individuals of the other population. This allows two similar species to coexist.