A wild-born, pure Australian desert dingo has taken out first place in the World's Most Interesting Genome competition.

A wild-born, pure Australian desert dingo called Sandy Maliki has taken out first place in the World's Most Interesting Genome competition.  As a rare, wild-born pure dingo, Sandy provides a unique case study. Pure dingoes are an intermediate between wild wolves and domestic dogs, with a range of non-domesticated traits. Sequencing Sandy's genome will help pinpoint some of the genes for temperament and behavior that undergo the transition from wild animals to perfect pets. The dingo sequencing project will be the first to test Charles' Darwin's 1868 theory that the process of domestication can be divided into two steps: unconscious selection as a result of non-intentional human influences; and artificial selection as a result of breeding by humans for desired traits. The main point of the annual international PacBio competition is to raise public awareness of science and how genomic research can benefit society. 
Original article here
More information on Sandy

Promiscuity and Decline of Evolution

“Survival of the fittest” and Darwin’s theory of evolution suggests that new species evolve when favored characteristics are bred and passed on more successfully than non-favored genes. Mating is thought to be through sexual selection. This is when one sex chooses to mate with the opposite sex because of very specific characteristics that will eventually form a new species. New research now suggests something other than the theory of evolution is driving mating and slowing down species evolution. Polygamous birds, ones that mate with several partners during a season, are less diverse genetically when compared to monogamous species. Rapid diversification does not equal higher genetic differences in population. As first scientists thought that polygamous birds choose their mates randomly but it seems they have a “type”. Humans prefer blonde or dark hair partners and the same rings true for birds. I find it interesting how other animals besides humans look for traits in mates that don't necessarily mean anything for survival. 

Original Article

Other Promiscuous Animals

Genetic Secret in Primrose Unlocked!

    More than 150 years ago, Charles Darwin studied the heterostyly in the primrose flowering plant (Primula vulgaris) and he hypothesized that since it's a plant species that two distinct flower forms (pins and thrums) in which the male and female reproductive organs were of different lengths, that it had co-evolved with insect-pollinators.

    Recently, scientists from the University of East Anglia have discovered exactly which part of the genetic code was responsible for this, though an event that occurred over 51 million years ago. The genes from the Primula genome were mapped and sequenced to find the specific gene cluster responsible for creating the different flower morphs. They discovered that the supergene directly responsible for this is the S locus. 


Primrose Flower

The S locus supergene is a tightly linked cluster of thrum-specific genes that are not in pins. The thrums were shown to be hemizygous, not heterozygous for the S locus. Therefore, the assumption that the homostyles arise by recombination between S locus haplotypes is false.The researchers were also able to determine that the original mutation occurred 51.7 million years ago. A floral homeotic gene was duplicated, then inserted itself in the S locus gene, and then mutated to control the anther position in the flower.

    This discovery is of major importance because it gives a better understanding of the pollination mechanism. Even though I was never very interested in plant biology, I found this discovery very eye-opening, especially since it unlocks the secret behind Darwin's observations and studies. I'm looking forward to reading more about this research and plant biology overall.

Links

• https://www.sciencedaily.com/releases/2016/12/161202074841.htm 
• http://www.nature.com/articles/nplants2016188

Biologists unlock 51.7-million-year-old Genetic Secret

Charles Darwin proposed a hypothesis "that some species with two distinct forms of flower, where male and female reproductive organs were of differing lengths, and evolved that way to promote out-crossing by insect pollinators". Darwin coined the term 'heterostyly' because of his understanding of the two forms of flower known as pins and thrums and succeeding studies aided in building the foundation of modern genetics.

Researchers at the University of East Anglia studies the genetic code of these species' to discover what makes them that way, through an event that happened about 51 million years ago. Professor Philip Gilmartin from UEA reported that they have pinpointed the supergene responsible for this phenomenon, on the S locus. Supergenes are a group of closely related genes that can typically have related functions. Researchers worked to sequence the genome of the Primula attempting to recognize the supergene responsible for the different flower morphs.

Professor Gilmartin explained that his team found more than just the supergene, they found it is distinct to only one flower form, the thrum. He also stated that studying the genetics of flower development and reproduction can expand our knowledge of pollination which is the foundation of biodiversity and food security.

During the researchers pursuit for the genes in charge of heterostyly, they managed to date the original mutation to 51.7 million years ago. When they found the S locus, they discovered it was closely related to the gene responsible for being in command of the identity on pedals on a Primula flower. This gene was duplicated and inserted into the S locus and mutated to control the position of the anther in the flower.  The team was able to date how long ago the mutation occurred because they found the duplicated gene.

It's fascinating to read about the origins of different forms of flowers. I never thought that flowers had genes that expressed phenotypes the way humans do. Also, it's wonderful that this discovery could expand knowledge of food security which can improve the lives of humans. I hope to see study like this one carried out in the future on more species of flowers. One can never know what they will discover!

Darwin's Finches Revisited (Again)

In a new study published this week in Nature, researchers announce that they have just found/tracked the gene responsible for beak size in  finch species inhabiting the Galapagos islands. This research builds upon previous findings from the same researchers a year ago in which they found the gene that controlled beak shape.

By studying the evolution of a finch specie over the course of a drought in 2004-2005, they observed that the specie members with the largest beaks were ineffectively competing with another endemic finch species that had even larger beaks. As a result, they had a die off, leaving behind members that had the smallest beaks within their specie. Comparing the genetics of the finches that died with the ones that lived allowed them to pinpoint the gene that controlled beak size for that specie. This worked because the specimens were the same species, with the same beak, only differing slightly in size.

It's surprising to see just how much we can still learn from studying these finches, despite having known them since 1835 when Sir. Charles Darwin first observed them. I have no doubt that we will continue to learn more about biology by studying the organisms of the Galapagos for generations to come.

Tree of Life's New Look

The tree of life was first thought of in 1859 when Charles Darwin wrote “On the Origin of Species”, since than the tree of life has been studied and referenced, theoretically that is. The invention of DNA sequencing was first to change the way scientist theorized the tree of life. This was because DNA sequencing let scientist find the relationship between species through their genes. It was not until 1970 when Carl Woese of the University of Illinois and his colleagues first published a “universal tree of life”, which was presented with the three main trunks we all know, eukaryotes, bacteria, and archaea. When scientist wanted to add new species to the tree they faced a challenge because they did not know how to grow many of the single celled organisms in the lab. Researchers however, developed a way to conquer this challenge, by pulling pieces of DNA from the environment and piecing them together.

Jillian F. Banfield of the University of California, Berkeley and her colleagues have been using the DNA piecing together technique for awhile now and have assembled genomes of hundreds of microbial species. The problem now was to figure out where they fit into the tree of life. Their solution was to redraw the tree. This was done by selecting more than 3,000 species to study, which gave them a large enough sample of diversity, and studied DNA form 2,072 known species along with DNA from 1,011 species of newly discovered. With their new data they used a supercomputer to evaluate the possible number of new trees. They eventually found the one that best supported their evidence, which is the one presented today. With the new tree it shows how much bacteria have been over showed by the close relationship between eukaryotes and archaea.

This new tree can present new questions for scientists and brings a whole new look at life’s evolution. I never thought I would see something that has been looked at and taught the same for so many years. I grew up with almost all of my science classes presenting the same tree and giving the same evidence, but now there is a new perspective.

New 'Tree of Life' Diagram

A team of scientists have recently recreated the "Tree of Life" diagram. They extended the amount of organisms primarily under the bacteria branch because they have found such a vast amount in mud of meadow-lands. They pulled pieces of their DNA to be analyzed through a separated that separated each entry to create the new diagram. The new tree has a thinner branch for eukaryotes with archaeabacteria being shown as having a closer relationship between the two. They have selected 3,000 species to be on this new tree with over 1,000 being newly discovered species. However there is speculation that some of these species could be chimera which would have a mixture of DNA from more than one organism. There is also the debate of whether the bacteria branch has begun to plateau or if there is an astoundingly larger amount out to still be discovered.

Aesthetically, the tree looks a lot more interesting than what Darwin's original "Tree of Life" from his 1859 book "On the Origin of Species". There is so much more to the new diagram, and it gives a better idea of how vast the amount of bacteria there are especially in comparison to eukaryotes such as mammals. I believe that there are more bacteria to be discovered that will only belittle the amount currently depicted. With the advancement of technology discovering new species should be simple. I do find it peculiar how archaeabacteria is actually more closely related to eukaryotes as opposed to bacteria. Archaeabacteria seem like very simple organisms that do not have the same complexity of eukaryotes.

Figure 1. New "Tree of Life" Diagram.

Figure 2. Darwin's Original "Tree of Life" Diagram

Darwinian Mystery of Odd South American Mammals Solved by Protein Sequencing

A discovery that for 200 years remained a puzzle, has finally been resolved through new research led by the Natural History Museum, the American Museum of Natural History, and the University of New York. This "puzzle" involved the strange group of South America's native ungulates (hooved mammals) that Charles Darwin referred to as "the strangest animals ever discovered." Originally, it was thought by some taxonomists that these animals were related to elephants and other species with ancient evolutionary ties to Africa. As it turns out, these animals--which disappeared 10,000 years ago--are actually related to mammals like horses.

This discovery was based on fossil protein sequencing, rather than DNA sequencing. Because DNA molecules deteriorate in warm, wet conditions, which is the climate in South America, scientists turned to investigate proteins instead. They did so by analyzing the collagen of these mammals. Collagen, which is a structural protein found in all animal bones, can survive for over millions of years in a wide range of conditions. Because specific coding sequences found in the organism's DNA control the chemical structure of the amino acids that make up these proteins, scientists have used this relationship between proteins and DNA to compare how closely related these animals are to other species. In other words, the amino acid composition in different species can be compared with that of the ungulates in order to understand how closely related the different species are.

The scientists involved in this research used proteomic analysis to screen 48 fossils of two species--Toxodon platensis and Macrauchenia patachonica--of which were the same species that Darwin discovered 180 years ago in Uruguay and Argentina (their remains only). They were able to acquire 90 percent of the collagen sequence for both species, and showed that their closest relatives were the perissodactyls--this is the group that includes horses, rhinos, and tapirs, which makes them a part of Laurasiatheria. What is very interesting about this resolved discovery is that the ancestors of these South American ungulates must have originated from North America more than 60 million years ago. This would have been around the time during the mass extinction, which killed off non-avian dinosaurs and other vertebrates.

Original article: click here.
Related article before the discovery: click here.