Thursday, November 19, 2009

Kipungi Hybridization Revisited

Recently, two simultaneous studies came to the conclusion that the close relationship of Rungwecebus kipungi to Papio (based on mitochondrial DNA) suggest a hybrid history for the genus/species. Burell et al. 2009 suggest that the kipungi was the result of hybridization between male mangabeys (probably Lophocebus) and female baboons. Zinner et al. 2009, on the other hand, suggest the possibility that the kipungi is a basal member of the Papio clade and fairly recently (until 0.35 million years ago) male kipungis were breeding with female baboons. In this study, Roberts and colleagues include DNA from a separate population of kipungis and find that only one population shows signs of hybridization, suggesting that the originally sampled population did, in fact, hybridize as Zinner and colleagues suggested. However, the newly sampled population shows no signs of hybridization, suggesting that the origins of kipungis were not results of mangabey/baboon hybridization.

Tuesday, November 10, 2009

A common variation in EDAR is a genetic determinant of shovel-shaped incisors

The association of EDAR 1540C with dental morphology is investigated, and the study indicates that the number of EDAR 1540C alleles is correlated with tooth-shoveling grade. Read all about it!

Global Microsatellite Content Distiguishes Humans, Primates, Animals and Plants

Galindo and colleagues show that global microsatellite content varies predictably by species, with most major differences occurring in developmental regions. Though further study is needed, they suggest that it might be fruitful to look at how global microsatellite content relates to different phenotypes.

Targets of Balancing Selection in the Human Genome

The authors looked at 13400 genes in two human populations for evidence of balancing selection; in particular, they looked for evidence of excess polymorphism and intermediate-frequency alleles. They find 60 candidate genes, and not surprisingly, many factor into immune function, though others encode keratin and membrane channels. Interestingly, they also find possible evidence for population differences in balancing selection between the two groups in 13 of the candidate genes.

Sunday, October 25, 2009

Heritability and Demographic Analyses in the Large Isolated Population of Val Borbera Suggest Advantages in Mapping Complex Traits Genes

Genetic studies performed on heterogeneous populations make identifying rare variants for complex diseases difficult because of confounding variables associated with heterogeneous populations. This study collected genetic samples and medical information for 1803 people within a relatively isolated population. The authors report that analysis of the isolated population reveals significant heritability of medically relevant traits that might not have otherwise been uncovered with a more heterogeneous cohort.

Human DNA methylomes at base resolution show widespread epigenomic differences

Human genetic variation extends beyond differences in the underlying genetic sequence. A recent study reported in Nature provides a more robust understanding of DNA cytosine methylation, an alternate source of genetic variation. While DNA methylation was primarily associated with repeat CpG (Cytosine-phosphate-Guanine) rich portions of the genome, Lister et al. report that approximately 25% of methylation in embryonic stem cells occurs in non CpG portions of the genomes. CpG regions are associated with promoter regions of genes, and methylation of these regions are thought to regulate gene expression. The report of methylation in non CpG regions raises new questions about the role of this epigenetic modification. The publication also represents one of the first papers describing a relatively complete map of the human epigenome.

Saturday, October 24, 2009

A new primate phylogeny

The authors present a new primate phylogeny inferred from a supermatrix of mitochondrial and nuclear DNA. They also present dates of divergence and diversification rates for major clades in the order.

Where's the ecology in molecular ecology?

The authors review the types of papers published in journals such as Molecular Ecology and conclude that, in general, these journals aren't living up to their titles. Most papers are evolutionary rather than ecological. They highlight major questions in molecular ecology (the field of study) that are being addressed, as well as suggest future directions for molecular ecologists. Finally, they state that all ecologists need to be molecular ecologists in some shape or form if they are to completely understand patterns and processes in ecology.

Monday, October 19, 2009

Two Main Bottleneck Events Shaped Modern Human Genetic Diversity

Humans are widely thought to have expanded out Africa starting approximately 50,000 years ago. In this process, genetic variation was reduced the further populations moved away from Africa due to successive bottleneck events. The frequency and nature of these bottleneck events have already been extensively explored in the literature. A recent study, which analyzed 783 microsatellite loci genotyped on 53 globally representative populations, concludes that two major bottleneck events occurred in human history – the first occurring as humans moved out of Africa and the second as humans moved across the Bering Strait into the New World. These events can be detected due to the genetic implications of bottleneck events. After sharp declines in population numbers, excess heterozygosity exists in the population than would be expected given the number of alleles remaining. The authors used the program ‘Bottleneck’ to detect this signature. This study reconfirms the conventional understanding of human expansion.

Sunday, October 18, 2009

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

This report describes a method called Hi-C which can be used to map the dynamic configurations of whole genomes by coupling proximity-based ligation with massively parallel sequencing.

Monday, October 5, 2009

Mutations in LOXHD1...distrupt hair cell function, cause progressive hearing loss

Mutations in LOXHD1, an evolutionarily conserved stereociliary protein, distrupt hair cell function in mice and cause progressive hearing loss in humans. Findings suggest that age-dependent hair cell failure is a common mechanism for progressive autosomal-recessive nonsyndromic hearing loss (ARNSHL).

Sunday, October 4, 2009

Aging is RSKy Business

Science Magazine is dedicated to Ardipithecus ramidus this week, but I thought this review article was worth a look too. It discusses current research into longevity and the possibility of intervening in the human aging process.

Thursday, October 1, 2009

Ardipithecus ramidus

After 15 years of excavation and analysis, the folks working in Middle Awash, Ethiopia have finally published the description and interpretation of the anatomy and functional morphology of Ardipithecus ramidus. The have a partially complete female skeleton as well as bits and pieces of other individuals. They interpret "Ardi" as a dietary generalist who walked upright (though not like we would) on the ground, moved much like Old World monkeys in the trees and was fairly sexually monomorphic.

Sunday, September 27, 2009

Kipunji Monkeys

An older article...but the recently discovered kipunji mokey seems to be closely related to baboons, sharing both nuclear and mitochondrial DNA with the genus Papio. It is suggested that they might in fact be a hybrid of Lophocebus mangabeys and Papio babboons.

There's no looking back (evolutionarily speaking)

The authors show that the evolutionary pathway of the vertebrate glucocorticoid receptor is most likely inaccessible to selection in the reverse direction.

Variance in mtDNA Among Bantu-speaking Populations

A study of mitochondrial DNA in two large Bantu-speaking groups, the Shona and the Hutu, shows that both groups display nearly all of the haplogroup markers characteristic of Bantu-speakers. Dispersal Bantu-speaking peoples in Africa was likely a gradual process, as evidenced by the pattern of genetic variability shown in this paper. However, some notable differences in mtDNA haplogroup composition seems to suggest that there was continued gene flow between already dispersed Bantu-speaking groups, as well as between Bantu and non-Bantu speaking groups. Interestingly, such variability was not found on the Y chromosome. Might this be explained by marriage and settlement patterns?

Friday, September 25, 2009

For all you Callithrix jacchus fans out there... now have microsatellite DNA markers and their chromosome assignment. The authors also demonstrate that blood samples are inappropriate for DNA genotyping because of blood chimeras.

Wednesday, September 23, 2009

Reconstructing Indian population history

The authors found great genetic diversity among Indian groups (greater than that observed within Europe). They suggest that this is a result of many founder events followed by limited gene flow. They also found evidence that two populations (one is closely related to Europeans and Central Asians, the other is closest to the Onge of the Andaman Islands) are ancestral to most current Indian populations.

Tuesday, September 22, 2009

Wednesday, September 16, 2009

Gene therapy fixes color blindness in monkeys

HuGE Navigator

This site will be useful for looking up candidate genes: a "searchable knowledge base of genetic associations" (thanks Sameer!)

Sunday, September 13, 2009

recent positive selection on genes associated with/linked to male pattern baldness

From the paper (AGA = pattern baldness):

Interestingly, it is the AGA risk haplotype that
shows evidence for positive selection in the European
population. The AGA risk haplotype also carries a derived
non-synonymous allele (57K) in the flanking ectodysplasin
A2 receptor gene (EDA2R). The 57K allele may have been
the target of positive selection in East Asians: it shows
large allele frequency diverences between populations,
lies in a likely functional domain of the
EDA2R protein, and the ancestral allele, 57R, is conserved
from human to rat. Thus, the AGA risk haplotype may have
hitchhiked to high frequency in Europeans as a result of
positive selection on the linked 57K allele in EDA2R

Tuesday, September 8, 2009

Where Did All the Flowers Come From? Flower Genomics

Nice review of the evolution of flowering plants, and increasing complexity of their origination. Without angiosperms, no primates...?

Thursday, September 3, 2009

Recent de novo origin of human protein-coding genes

. . . human-specific protein-coding genes originating from ancestrally noncoding sequences.


Fossil feather coloration

Yale researchers identify melanosomes in a fossil feather. Color is difficult to establish, but provides evidence of pigmentation that was previously just artistic license.

Saturday, August 29, 2009

TREE paper countering Patterson et al

original Patterson et al nature paper HERE

more interesting candidate genes: size, longevity, behavioral stereotypes

This dog study is > a year old, but I only just discovered it:

Candidate genes associated with size, longevity, and behavioral stereotypes of dogs (New Scientist seems esp interested in high strung chihuahuas)

Friday, August 28, 2009

adaptive coloration in deer mice

Another cool study from the Hoekstra lab: A single amino acid deletion influencing (or linked to something influencing) agouti expression in Nebraska deer mice.

Thursday, August 27, 2009

Linus Pauling quote

"The way to get good ideas is to get lots of ideas, and throw the bad ones away"

genetics of dog hair (length and curl)

new Science Express paper from Ostrander lab: Variation in dog coat phenotypes largely due to mutations at just 3 genes (RSPO2, FGF5, and KRT71).
This is exciting -- for several reasons!

here is an NPR snippet about the article (thanks for tip, Monica):

Friday, August 21, 2009

hamadryas genome

wow, I didn't realize a draft assembly (almost 6x) of the hamadryas genome is already out.

Thursday, August 20, 2009

DNA from difficult samples

new way to extract DNA from poor / contaminated samples:
Won't work with the QIAcube, but something to keep in mind...

Wednesday, August 19, 2009

sleep genes

I think I might have fixed the links problem...

I'll test it with this science article (tip from Jason) on the DEC2 gene and the evolution of sleep
-- surely some diurnal vs cathemeral vs nocturnal projects there...

Link's don't work?


Times story:

Study page:

Redheaded pain

I'm sure you've all seen this, but:

MC1R mutation may lead to increased pain sensitivity as well as red hair. My question: is it the MC1R, or is it some other associated gene/linkage?

I now feel even worse for red colobus monkeys.



Tuesday, August 18, 2009

CI Primate field guides

Exciting-- In addition to the Lemurs of Madagascar, CI now has a range of pocket field guides with illustrations by Stephen Nash. And they are affordable - $7.95 each including shipping!