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Posts Tagged ‘evolution’

Ever wonder what the difference is between Ale vs. Lager yeast?

October 22, 2014 2 comments

Despite being a yeast researcher, and supposedly having a pretty good handle on yeast genetics, I have always struggled to fully understand what the underlying genetic differences are between ale and lager yeasts. Thanks to a great article by Martha Harbison from Popsci, and research done by Libkind et al, I have finally figured it out!

Generally ales are fermented warmer with”top fermenting” yeast, and produce more fruity esters as a result. Lagers tend to be fermented cooler with “bottom fermenting” yeast, and produce more “reductive” or sulfur characters.

Ale vs. Larger

This description, while great for brewers was always unsatisfactory to me as someone with an interest in genetics and taxonomy. This was further complicated by the interchangeable use of S. calsbergensis and S. pastorianus. Top fermenting yeast are generally just plain old Saccharomyces cerevisiae. Bottom fermenting yeasts are generally more variable and have allotetraploid chromosomes, i.e. 4 chromosomes made up of mixed up bits and pieces of different yeast genomes.

So, where the hell did lager yeast S. pastorianus come from? And why did it only show up in the 1500s, thousands of years after humans figured out how to brew with S. cerevisiae? The answer came in 2011, with the publication of “Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast” by Libkind et al in Proceedings of the National Academies of Sciences. In it, the researchers analyzed 6 yeast genomes: S. pastorianus, S. cerevisiae, two contaminant Saccharomyces species found in breweries, S. bayanus and S. uvarum, and two wild strains. The scientists knew through prior research that Saccharomyces species thrive on oak trees in Europe. After collecting samples from forests all over the world, they isolated two cold-tolerant yeast strains from the forests of Patagonia in Argentina.

After analyzing the genomes of these cold-tolerant strains, the researchers discovered that they were members of an entirely new species of Saccharomyces yeast, which they namedSaccharomyces eubayanus. The “eubayanus” part is interesting, because what the scientists also determined in this study is that the contaminant strain S. bayanus found in the European brewing environment isn’t, as previously thought, actually its own species. It is a domesticated hybrid strain of this Patagonian yeast. The “eu” part of “eubayanus” is to indicate that the Patagonian strain is the pure progenitor species.

From Eubayanus to Pastorianus Ale yeast and yeast from the forests of Patagonia met in a brewery…and lager was born! 

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

Diego LibkindChris Todd HittingerElisabete ValérioCarla GonçalvesJim DoverMark JohnstonPaula GonçalvesJosé Paulo Sampaio

Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate itSaccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry inNothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

Some of this can be summed up by this figure from:

Saccharomyces diversity and evolution: a budding model genus

Chris Todd Hittinger

Relationships of the seven natural species of Saccharomyces and their key industrial hybrids. Populations and lineages that are not regarded as distinct species are discussed in the text but not shown. Note that the S. bayanus species complex includes two natural species (S. uvarum and S. eubayanus) and two hybrids that had been given species names (Saccharomyces pastorianus and S. bayanus).

Basically it seems like S. pastorianus evolved through the actions of human beings and hybridizations of different Saccharomyces species in the context of brewing.

Here is a spread sheet of compiled strain comparisons from different companies. Mostly beer oriented, and very helpful: YeastBot Database thanks to u/Oginme for posting it.

This leads me to a final question: did we select yeast, or did yeast select us?

-Gordon Walker

Got ugly mug, at least you can take a punch! Males have facial features that were selected to stand up to getting punched

June 9, 2014 Leave a comment

Interesting, if slightly controversial argument that male faces (and other features) were selected through the course of evolution to be more resistant to impacts from violent altercations. Fascinating idea, but I would still cry like a baby if you clocked me right in the face.

Excerpt from “Male faces ‘buttressed against punches’ by evolution” By Jonathan Webb

Fossil records show that the australopiths, immediate predecessors of the human genus Homo, had strikingly robust facial structures.

For many years, this extra strength was seen as an adaptation to a tough diet including nuts, seeds and grasses. But more recent findings, examining the wear pattern and carbon isotopes in australopith teeth, have cast some doubt on this “feeding hypothesis”.

Instead of diet, Prof Carrier and his co-author, physician Dr Michael Morgan, propose that violent competition demanded the development of these facial fortifications: what they call the “protective buttressing hypothesis”.

“Jaws are one of the most frequent bones to break – and it’s not the end of the world now, because we have surgeons, we have modern medicine,” Prof Carrier explained. “But four million years ago, if you broke your jaw, it was probably a fatal injury. You wouldn’t be able to chew food… You’d just starve to death.”

The jaw, cheek, eye and nose structures that most commonly come to grief in modern fist fights were also the most protected by evolutionary changes seen in the australopiths.

Furthermore, these are the bones that show the most differences between men and women, as well as between our male and female forebears. That is how you would expect defensive armour to evolve, Prof Carrier points out.

“In humans and in great apes in general… it’s males that are most likely to get into fights, and it’s also males that are most likely to get injured,” he told BBC News.

 

 

Related articles:

Protective buttressing of the hominin face 

David R. Carrier and Michael H. Morgan

When humans fight hand-to-hand the face is usually the primary target and the bones that suffer the highest rates of fracture are the parts of the skull that exhibit the greatest increase in robusticity during the evolution of basal hominins. These bones are also the most sexually dimorphic parts of the skull in both australopiths and humans. In this review, we suggest that many of the facial features that characterize early hominins evolved to protect the face from injury during fighting with fists. Specifically, the trend towards a more orthognathic face; the bunodont form and expansion of the postcanine teeth; the increased robusticity of the orbit; the increased robusticity of the masticatory system, including the mandibular corpus and condyle, zygoma, and anterior pillars of the maxilla; and the enlarged jaw adductor musculature are traits that may represent protective buttressing of the face. If the protective buttressing hypothesis is correct, the primary differences in the face of robust versus gracile australopiths may be more a function of differences in mating system than differences in diet as is generally assumed. In this scenario, the evolution of reduced facial robusticity in Homo is associated with the evolution of reduced strength of the upper body and, therefore, with reduced striking power. The protective buttressing hypothesis provides a functional explanation for the puzzling observation that although humans do not fight by biting our species exhibits pronounced sexual dimorphism in the strength and power of the jaw and neck musculature. The protective buttressing hypothesis is also consistent with observations that modern humans can accurately assess a male’s strength and fighting ability from facial shape and voice quality.

 

 

Pattern, severity and aetiology of injuries in victims of assault.

Although the incidence of assault and other violent crime is increasing in the UK, the cause and overall pattern of injury, and the need for admission have not been defined in adult victims who attend hospital. In a prospective study, all 539 adult victims of assault attending a major city centre Accident & Emergency department in 1986 were therefore interviewed and examined. Facial injury was extremely common: 83% of all fractures, 66% of all lacerations and 53% of all haematomas were facial. The upper limb was the next most common site of injury (14% of all injuries). Twenty-six per cent of victims sustained at least one fracture and nasal fractures were the most frequently observed skeletal injuries (27%) followed by zygomatic fractures (22%) and mandibular body (12%), angle (12%) and condyle (9%) fractures. Seventeen per cent of victims required hospital admission. Overall, the type of injury observed correlated with the alleged weapon used (P = less than 0.001) though 20% of victims who reported attacks with sharp weapons sustained only haematomas or fractures. Injury most often resulted from punching (72% of assaults) or kicking (42% of assaults). Only 6% of victims reported injury with knives but 11% were injured by broken drinking glasses. Those who were kicked were most likely to need hospital admission.

 

57 year experiment, Drosophila kept in dark for 1400 generations, many evolutionary changes (record longest postdoc!)

April 30, 2012 2 comments

Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

Minako Izutsu1,2#, Jun Zhou3, Yuzo Sugiyama1, Osamu Nishimura1, Tomoyuki Aizu4, Atsushi Toyoda4, Asao Fujiyama4, Kiyokazu Agata1,2, Naoyuki Fuse1#*

1 Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan, 2 Laboratory for Molecular Developmental Biology, Graduate School of Science, Kyoto University, Kyoto, Japan, 3 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America, 4 Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan

Link to original paper in PLoS

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

Amazing experiment by Izutsu et al. where they kept flies in the dark for 57 years and then sequenced them. Goes a long way in explaining evolution of traits under certain conditions: think cave dwelling animals. Score one for evolution.

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