It is all in the eyes: Eye coloration in Humans and wild animals

Humans and domesticated animals tend to show variation in eye color unlike in wild animals whose eye colors is usually fixed. It is however not known when this variation in eye color emerged in the evolution of the genus Homo and domesticated animals. From previous research, we know however that the emergence and fixation of variants in both coat, plumage and eye coloration started during the early stages of domestication in the Neolithic. Eye coloration in humans is known to be continuous having numerous shades ranging from different shades of light blue to dark brown. The very rare cases of eye coloration in wild animals is associated with maturation with age as seen in birds and some instances of sexual dimorphism (certain duck species). Who knows perhaps in humans it is a case of sexual selection with blue and green eyed individuals preferred more as mates than brown eyed individuals.

News Article: here

Research Article: here

Joanne

3D printing human skin pigmentation

A recent paper in a journal call Biofabrication (?!) describes a method for printing "pigmented human skin constructs". Although this was only a proof-of-concept paper, the ultimate application would be for pigment-correct skin grafts.  That sounds pretty great, actually.

Using hybrid zones to identify loci associated with coloration

A recent study used the natural admixture in a hybrid zone to study the traits based on carotenoids.  Carotenoids, along with melanin pigments, determine the coloration of birds.  SNPs were identified for five plumage traits which are located in regions which are enriched for keratin filaments (the fibrils which make up feathers).  The carotentoid-based trait which is associated with throat color has more than a dozen regions of association in the genome.  The gene SCARF2 was identified as a candidate for carotenoid processing.  Additionally, two melanin-based traits, coloration of eye line and eye-spot, were found to map to a single genomic region.

Genes responsible for diversity of human skin colors identified

A study of within-Africa variation in skin color has demonstrated that the huge level of diversity is linked to previously-undescribed regions of the genome that seem to have been present for several hundred thousand years. Previous work has hypothesized that variation in skin pigmentation is adaptive for sun exposure. The regions of the genome described here also seem to be linked to the lower risk of Africans for melanoma. In terms of human evolution, an interesting finding noted that  the older version of these variants in many cases was the one associated with lighter skin, suggesting that perhaps the ancestral state of humans was moderately pigmented rather than darkly pigmented skin.

News article here: https://www.sciencedaily.com/releases/2017/10/171012143324.htm

Kim Foecke

Rare Yellow Cardinals and White-Patched Mice

A rare yellow-feathered cardinal sits in an Alabama tree Feb. 17, 2018.
(Jeremy Black)

I. Several outlets (including the Chicago Tribune and Smithsonian magazine) recently reported on a rare bird sighting: a yellow male cardinal in Alabama. While females are generally more of a dull red or rust to the males' vibrant red, yellow coloration is abnormal for both sexes. Researchers suggest the bird's rare pigmentation may be due to a mutation in the CYP2J19 gene, which is responsible for red pigments in cardinals and other birds and insects (interestingly, the team that discovered this gene is also learning how birds create structural, not pigmented color). If not a mutation, the other hypothesis is that this cardinal is suffering from malnutrition and/or environmental stressors, which could impact the production of the color-converting enzymes... interesting that across species yellow is considered a signal of sickness (thinking jaundice, etc.).


II. I'm going to talk more about domestication later, but wanted to share this recent article in Science as it is also relevant to our pigmentation/coloration discussion. Here the authors show that wild mice living in a space relatively void of predators and with ample access to food and water became "tamer", and that with that increased tameness, white spots of fur emerged out of the traditional russet color. Over a period of six years the proportion of adult mice with white fur more than doubled. They claim this is significant because it occurred without human intervention, in other words, a case of self-domestication. I have issues with what they are claiming as "non-human" aided domestication, but still an interesting study.

-Courtney

Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars

Parrots are some of the most phenotypically diverse creatures on the planet. They can be all sorts of colors. This recent paper focuses on the red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars(Parakeets) have been extensively bred for plumage traits during the last century. The authors of this paper attempt to use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation. The findings concluded that the blue trait maped to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS). The researchers then used yeast in with MuPKS, and found that the yellow pigments accumulated. The yellow pigments found in the yeast were confirmed by mass spectrometry to match those found in feathers. The R644W substitution abolished MuPKS activity. The researchers concluded that parrots aquired their colors through regulatory changes that cause high expressions of MuPKS in feathers.


Article
Forbes Article

- Louis

PopCorn: Genome Biology

A history of male migration in and out of the Green Sahara

Climate change and developments in technology are two under reported and explored areas of human subsequent migrations out of Africa, after what is often refereed to as the "migration out of Africa" event A  recent study claims human Y-chromosomal lineages that flourished in this Green Sahara and their relation to present-day populations are evidence of a once fertile Green Sahara, complete with lakes, savannas and animals. 

• Yali XueEmail author

Genome Biology201819:30

https://doi.org/10.1186/s13059-018-1410-8

©  The Author(s). 2018

Published: 13 March 2018

Popcorn: Post One- Carly Johnson

Regulatory pathway analysis of coat color genes in Mongolian horses

Unlike previous work that focused on gene polymorphism, the current research evaluates the impact of gene expression on horses coat coloration. Skin samples were collected from horses with white and black coat colors and the genes were identified through the use of RNA sequencing. In this study Li and his colleagues were able to provide a collection of genes that are differentially expressed in horse skins of different colors. Their findings indicate that the genes such as DCT, HPD and TAT  are involved in tyrosine metabolism which is responsible for melanin production. The authors indicate that the deregulation of these genes is associated to formation of coat coloration and skin health issues

Here is the link of the original paper:

https://hereditasjournal.biomedcentral.com/articles/10.1186/s41065-017-0048-y

Axelle

Where have the Giraffe spots gone?!

Two giraffes have been spotted recently in Kenya without their spots! The Hirola Conservation Program, but not from congenital disorders like albinos, but from a genetic condition called leucism. Leucism results in the partial loss of color in an animal's skin, or hair, but not in other organs like their eyes. Leusicm means these animals can still have dark eyes, unlike their albino counterparts. Nat Geo also spotted a white moose in Tanzania's Taragire Nation Park, that has leucism, what gave away that he albino? Leucism left some colored spots! 

https://www.theverge.com/tldr/2017/9/17/16309394/white-giraffes-animals-leucism-albinism

Carly Johnson

The Many Shades of Pearls

A really interesting study looked at the phenotype variation in a model species P. margaritifera by examining the three way interaction between the donor oyster, recipient oyster, and the final cultured pear product. This particular species is a good model because of  it’s large range of pearl colors that is reflected by the large diversity of inner shell color phenotypes.  For this study they observed this phenotype variation at the macro, micro, and molecular level. Examining this at the molecular level showed that there were a series of gene encoding proteins, specifically genes related to aragonite formation, associated with the shell biomineralisation process that show significant differences in the donor phenotypes. Through a series of experimental grafting of the donor to recipient oyster species show that there is high amounts of inter-individual donor phenotype. 

For a more in depth analysis of this study see the original paper in Nature here.

-Sam

Tadpole Coloration and Predation

The authors of this article argue that in order to avoid predation, neotropical tadpoles exhibit several colorations. To test this hypothesis, researchers tested the effectiveness of predator avoidance in two amphibian species, Bokermannohyla martinsi--whose coloration is aposematic--and Ololygon machadoi--whose coloration immitates that of a water-living insect species. Conducting both in situ and ex situ experiments in which the two tadpole species were placed against a variety of background colors, researchers noted that O. machadoi suffered higher predation rates than O. machadoi. Researchers conclude that although predation by birds is occasional, tadpole coloration may impact the rates of predation on these two species of amphibians.

The link to the article can be found here

-Leanne

The Evolution of Butterfly Wing Coloration & Patterning

L: normal 'pink lady' butterfly wing.
R: CRISPR-altered mutant wing.
(Mazo-Vargas et al. 2017)

Dr. Anyi Mazo-Vargas and colleagues (including GW's own Dr. Arnaud Martin) found a single gene that alters a butterfly's wing pattern using a gene editing method called CRISPR/Cas9. The team detailed their finding in a recent paper in PNAS. The gene, WntA, was found to be involved in stripe patterning in 3 Vanessa species, and in creating boundaries for melanin and light-color patterning in two species of Heliconius. WntA paired with optix, another gene responsible for the development and evolution butterfly color and iridescence found by Zhang et al. 2017, are chief contributors for the "painting" of butterfly's wings.  As Arnaud Martin explained to Nature, the genes work together like a coloring book; WntA creates the lines, and optix fills them in with color.

For the full Anyi Mazo-Vargas et al. 2017 PNAS article, click here. For the Zhang et al. 2017 paper, click here.

- Angie

(Non-potluck post)->Genetic Mechanisms Mediating the Circadian Regulation of Sleep

Sleep is one of the crucial behaviors  characterizing living organisms including humans and it is suggested to be regulated by the organism's internal circadian biological clock. To have an improved understanding about this relationship, this recent paper published in Trends in Genetics, reviews the genetic implication in the circadian regulation of sleep and wake by comparing the findings generated from recent research on human, mice, zebrafish and fruitfies.  

Blum and his colleagues indicate the role played by the clock genes in sleep regulation . They show how knocking out clock genes in mice and flies results in sleep disturbance in these species. They also show how the change in the clock genes results in sleep disorders in human. For example, the mutation in the clock genes Period3 and Cryptochrome1 have been associated to delayed sleep phase syndrom in human. The gene mutant aanat2 which regulates sleep-controlling hormones such as melatonine  has also shown a negative effect on sleep as evidence by research conducted on zebrafish. The authors of this review continue to discuss the genetic mechanisms in neural excitability of sleep- wake circuits where the alteration of the genes regulating the clock neurons results in varying lengths of sleep.

Fig.1 Some of the genes involved in circadian regulation of sleep and their functions (The whole list is in the original paper)

You can find the published paper on the follwing link:

https://www.sciencedirect.com/science/article/pii/S0168952518300015

Axelle
First Non-potluck post
Paper (2018) from Trends in Genetics

Birds of a feather flock together, but will still become separate species overtime

Coeligena helianthea

Coeligena bonapartei

A preprint of study of two Andean neotropical hummingbirds, Coeligena helianthea (blue-throated starfrontlet) and the Coeligena bonapartei (Golden-bellied starfrontlet), with different plumage became separate species in spite of gene flow. Palacios and colleagues, the authors of this study, tried to identify the cause of the different plumage and speciation by testing the neutral markers of mtDNA and ultraconserved elements of nuclear DNA. They also examined the candidate gene MC1R which in previous studies of vertebrates has been associated with changes in the darkness and lightness of pigmentation and tested Glogers’ rule which predicts darker coloration will occur more often in humid environments as well as compared ecomorphological variables, such as physical adaptations of bills and wings to microhabitats and food resources.

Palacios and colleagues found very low genetic differences between the two species of hummingbirds which was expected due to the estimates of gene flow occurring. What was not expected was the phenotype differences is plumage color not caused by MC1R or Glogers’ rule. No difference was found the two species in their macroclimatic niches, but distinct differences in their ecomorphology, particularly in their wings.

The authors conclude the cause of speciation and plumage differences are due to other ecological pressures not examined in their study or sexual selection.  

Link to the preprint can be found here.

-Kristen Tuosto

Genetic basis of body color and spotting pattern in redheaded pine sawfly larvae 2 (Neodiprion lecontei)

Redheaded pine sawfly species is characterized by variations in color (yellow, white, and diverse spotting patterns), and coloration phenotypes are often used as cryptic and / or aposematic mechanisms to escape predators. To expand the existing sample of color loci, Linnen et al. performed quantitative trait locus (QTL) mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly, including carotenoid-based yellow body color and melanin-based spotting pattern. The QTL models explained a good proportion of phenotypic variation for both traits and suggested a defined genetic architecture that is neither monogenic nor highly polygenic. Then, using linkage map, they were able to identify promising candidate genes underlying the loss of yellow pigmentation in populations in the Mid-Atlantic/northeastern, and a reduction in black spotting in Great-Lakes populations

Link: http://www.genetics.org/content/genetics/early/2018/02/28/genetics.118.300793.full.pdf

Sylvain

Save the Bees: a (Non-Potluck) Article from Current Biology

"Save the bees" has become a common rallying call to the environmentally conscious. Even large corporations such as General Mills have joined in by offering free flower seed packs with specially marked boxes of Honey Nut Cheerios. Now, a recent article published in Current Biology looks at the molecular determinants of bee sensitivity to insecticides--specifically neonicotinoid insecticides--with the hope safe-guarding the health of bees. Previous studies have shown that not all neonicotinoids affect honey bees to the same degree, however specific genes and enzymes responsible for the magnitude of the bees' sensitivity to any given insecticide remained unknown. The authors demonstrate that the honeybee gene CYP9Q3 produces the cytochrome P450 which is responsible for the metabolizing of certain toxins found within neonicotinoid insecticides, thus decreasing the honeybee's sensitivity. Additionally, the authors found an equivalent gene, CYP9Q4 in bumble bees. Bees are vital to both the health of the eco-system, and economically important crops; this research may present a new pathway for bee conservation.

You can find the link to the article from Current Biology here

-Leanne Chambers

Leanne's First Current Biology Journal Update

(Non-Potluck Post) Interacting Species and Phylogenetic Comparison Methods

 

So I started to write this a couple of weeks ago, before our phylogenetics discussion, but as I'm just finally getting around to posting it, it is also relevant to our discussion this week. 

While we now commonly use phylogenetics to evaluate relationships between sister and more distantly related taxa, I thought this perspective on the lack of solid methods for using phylogenetics to look at species evolutions through the lens of coevolutionary relationships (i.e. varying types of mutualism, predator-prey, host-parasite, etc.) was interesting.

This paper discusses the difficulties of assessing multiple traits/interacting lineages and accounting for each individual phylogeny. The authors use the example of various fig species their fig wasp pollinators to "propose a new statistical procedure for evaluating the covariation between traits for two sets of interacting species while accounting for their respective phylogenies."

A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

-- Courtney

Non-Potluck Post

2nd Article from Evolution

Tree Trees, or Phylogenetics of Forests

An article in this week's Aiken Standard highlighted a new study that reshapes classification of relationships between and among flora across the world. Prior to the publication of the study, classification depended on counting species and determining similarity based on percent in common. Using phylogenetics, however, the authors are able to identify five major regions and their relationships. 

"Prior to the team’s study, the established hypothesis was that the Neotropics – including Central and South America – were different from the Paleotropics of Africa, Asia and Australia.

'But when we make these phylogenetic trees for each forest, we actually find that American forests and west African forests are more closely related to each other than they are to the Indo-Pacific,' DeWalt said."

This has implications for understanding how species in a given region may adapt to climate change, but could also give clues about the environments that early human and human ancestors survived in.


Here is the actual study from the Proceedings of the National Academy of Sciences.

--Courtney

Non-Potluck/Non-Journal... Love in the Time of Personal Genomics

Others may already have seen this, but it came out after our discussion on personal genomics and I thought it was just too over-the-top not to share. It seems the phrase "there's an app for that" really does apply to all... you can now use your DNA as a dating tool. Apparently with Pheramor you swab your cheek, send it in, and then based on your genes and personality traits, the company "populates your app with a carousel of genetically and socially optimized potential mates in your area". WHATEVER THAT MEANS.


Read more at Wired.

-Courtney

Divergence Age of Map Turtles

Map turtles are known to have experienced a rapid diversification leading to an uncertainty about their species boundaries, their phylogenetic relationship within the genus and timing of their divergence. Scientist used empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock. They found that the divergence and phylogeny times are suggested to have been more recent and more rapid. The results revealed that three major lineages of the map turtles (G. geographica, megacephalic clade, western clade) were found to be monophyletic while further analyses revealed that the map turtles are considerably younger than previously estimated with the crown age being 0.9224- 2.41 my. The megacephalic clade and western clade have identical crown ages suggesting that these two lineages became diversified shortly after becoming isolated from one another.

 https://www.sciencedirect.com/science/article/pii/S1055790317301598

JOANNE

Seeing the complicated SYMPHY forests through the trees

A review article in TREE proposes an interesting new framework for phylogenetics using symbiomes instead of individual species. This would basically create trees connected to other distant trees (e.g. fungi interacting with plants). Conceptualizing the multidimensional layers makes my head hurt. Because everything needs a snappy acronym, they're calling it SYMPHY (symbiome phylogenetic).

Risk Sensitivity and Phylogenetic Reconstruction

Working with four chimpanzees, the authors of this paper challenge the idea of the use of species specific behavior in phylogenetic reconstructions, specifically in regards to risk sensitivity. Studies in primate risk sensitivity have been conducted with phylogenetic goals, such as determining risk preferences for a single primate species or a group of primate species. This has lead to lemurs being characterized as risk averse and chimpanzees being characterized as risk prone. In order to challenge this idea, the authors tested four chimpanzees preferences to different feeding stations that changed via mean reward quantity, reward type, context, and experimental designs. The authors noted that chimpanzee preference and risk changed based off of these differences. The authors concluded that risk sensitivity changes between individuals based off of the context of risk and the individuals present. The authors close note that this is not conducive to assessing species specific behavior or constructing/enforcing phylogenies.


You can find the link to the article here

-Leanne

The phylogenetic roots of human lethal violence

https://www.nature.com/articles/nature19758

Carly Johnson

This article argues that aggression in mammals has a significant phylogeny component, and the level of violence we experience today in human populations is the same as we would expect to see in prehistoric bands or tribes. It is commonly accepted that violence has a culturally inherited trait, but it is also has a highly heritable human trait. The change in violence however has occurred with time due to sociopolitical organization of human populations. This study was preformed via lit review from one data set.

FYI: conspecific means (of animals or plants) belonging to the same species- perhaps I am the only one that didn't know this, but just in case.

Conservation of Enhancer Regulation in Primates

In the news article posted on phys.org, the phylogenetic study by researchers at Cold Spring Harbor Laboratory and Cornell University to investigate specific roles of enhancer transcription factors in primate evolution. The news article focuses on the basic concept of evolutionary conservation, however the research article published about the findings of the experimentation is more elaborate. The researchers measured nascent transcription of resting and activated CD4+ T cells in multiple human, chimpanzee, rhesus macaque, and rodent individuals to circumvent post-transcriptional interference. They measured overall conservation with species-specific irregularities, especially at distal enhancers and non-coding RNAs. They also noted that genes regulated by more enhancers tended to have more conserved expression profiles. Finally, the researchers identified mutations causing human-specific transcription and experimentally validated their findings.

- Evan Holmes

Complete mitochondrial genome of an olive baboon (Papio anubis) from Gombe National Park, Tanzania

Roos and his colleagues report a sequencing of a complete mitochondrial genome of an olive baboon from Gombe. The genome sequenced has a length of 16,490 bp and exhibits the typical structure of mammalian mitochondrial genomes. The results revealed that the olive baboon from Gombe forms a strongly supported sister lineage to a clade consisting of eastern Papio anubis, northern Papio cynocephalus and Papio hamadryas, thus, further supporting the previously detected polyphyly of olive baboons

Link: https://www.tandfonline.com/doi/pdf/10.1080/23802359.2018.1437813?needAccess=true

Sylvain

Phylogeny, molecular dating and zoogeographic history of the titi monkeys (Callicebus, Pitheciidae) of eastern Brazil

A recent research investigated the validity of the taxonomy of Titi monkeys endemic of South Amerika . The results of the study indicate that at about 12 Ma, the ancestor of these New World primates occupied a wide area in South Amerika extending from the Amazon forest to the South of the Atlantic forest. It is suggested that Callicebus genus diverged from the amazonian titi monkeys during the late Miocene when the Savannah arose and separated the two forests. Through the DNA analysis, the results confirm the classification of the genus Callicebus which diversified in 5 species at about 5 Ma.

Published paper: https://www.sciencedirect.com/science/article/pii/S1055790316304250

Axelle

Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

Scientists have traced the origin of the disease Pseudogymnoascus destructans, a fungal pathogen causing the epizootic of white-nose syndrome in North American bats. The researchers used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies. White-nose syndrome was traced back to Eurasia where researchers claim the disease was present for millenia. Eurasian bats - unlike their North American cousins - are believed to have evolved a resistance to the disease. These findings provide hope for all North American bat species as researchers claim that it is possible these populations will also evolve resistance to the fungus in the future.

Article

- Louis Gorgone