genetics
edyong | September 18, 2009The two-toed sloth is a walking hotel. The animal is so inactive that its fur acts as an ecosystem in its own right, hosting a wide variety of algae and insects. But the sloth has another surprise passenger hitching a ride inside its body, one that has stayed with it for up to 55 million years - a virus.
In the Cretaceous period, the genes of the sloth's ancestor were infiltrated by a "foamy virus", one of a family that still infects humans, chimps and other mammals today. They are examples of retroviruses, which reproduce by converting an RNA genome into a DNA version and inserting that…
nisbetmc | September 17, 2009
I am in Banff this week participating in a fascinating workshop on the scientific, clinical, ethical, and communication issues related to personalized medicine and genomics. A special issue of the journal Public Health Genomics (formerly Community Genetics) will focus on the themes covered at the workshop. I will be contributing a review article on research and issues related to the media and public engagement. Early access publication of the articles should occur in the spring.
On a related topic, earlier this week, the Columbia Journalism Review posted a commentary that I co-authored…
razib | September 17, 2009I asked readers to fill out a survey a week and a half ago. Results are in.
gregladen | September 17, 2009The evolutionary history of mammals can be reviewed as the evolutionary history of tooth loss. The early mammals had many teeth, and every now and then in evolutionary time, a tooth is lost wiht subsequent species arriving from that n-1 toothed form having that smaller number of teeth. With ver few exceptions, no mammals have added a tooth during the history of mammals. (Excepting maybe the very very earliest period, but probably not.)
Well, the loss of enamel itself is also an evolutionary trend in mammal history, and recent research published in PLoS Genetic associates genetic changes…
edyong | September 16, 2009People with red-green colour blindness find it difficult to tell red hues from green ones because of a fault in a single gene. Their inheritance robs them of one of the three types of colour-sensitive cone cells that give us colour vision. With modern technology, scientists might be able to insert a working copy of the gene into the eye of a colour-blind person, restoring full colour vision.
You might think that the brain and eye would need substantial rewiring to make use of the new hardware, but Katherine Mancuso from the University of Washington thinks otherwise. She has used gene…
razib | September 15, 2009
One of the problems with human genetics where it resembles economics are the ethical issues involved in experimentation. Luckily for science, but unluckily for individuals, medicine offers many "natural experiments." But in the area of population genetics and history analyses of pedigrees or family based studies centered around particular traits and genes have limitations of scale. Luckily for science again, and unluckily for millions of Amerindians and black Africans, Latin America offers a cornucopia of possibilities when it comes to exploring the outcomes ensuing from admixture between…
razib | September 14, 2009Nearly 50 years ago W. D. Hamilton published two papers, The genetical evolution of social behaviour - I & The genetical evolution of social behaviour - II, which helped revolutionize our conception of how social and genetic process might work in concert. It opened up a field of research which was highlighted in Richard Dawkins' The Selfish Gene, and helped make inclusive fitness a general idea which allows us to view specific phenomena through a powerful theoretical lens. Hamilton's original work was broad in its implications and abstract in method, but concretely utilized various…
razib | September 12, 2009The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes. The authors are Russian, so I think the somewhat grand and archaic first portion of the title can be explained as a mater of translation. Here's the author summary:
The primate centromere evolves by amplification of alpha satellite sequences in its inner core, which expands and moves the peripheral sequences sideways, forming layers of different age in the "pericentromeric" area. The expanding centromere model poses two main questions: (1)…
razib | September 8, 2009Update: Author comments below.
PLoS ONE has an interesting paper out, Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico. They're exploring the topic of African ancestry and hypertension, which seems to have a positive correlation, but where there is dispute as to whether that correlation is driven only by genes, or environment, or a combination. Puerto Rico is characterized by a wide range in admixture between Europeans & Africans (with a minor but significant amount of Amerindian). Additionally, because most variance in…
razib | September 8, 2009If you have a minute, I'd appreciate it if you fill out this survey, the 6 questions should take 30 seconds (2 optional questions about where you came from to take the survey). This is for a friend's research project. The results will be posted next week.
razib | September 8, 2009There's been some buzz over a recent paper, mtDNA Data Indicates a Single Origin for Dogs South of Yangtze River, less than 16,300 Years Ago, from Numerous Wolves. This is tracing the maternal lineage, and suggests that that lineage is most diverse in southern China (just as human lineages tend to exhibit the most diversity in Africa). Here's the abstract:
...We therefore analysed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution, and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture…
razib | September 7, 2009Another study on obesity & Africans, with a slight twist, Admixture Mapping of Obesity-related Traits in African Americans: The Atherosclerosis Risk in Communities (ARIC) Study:
Obesity is an important cause of morbidity and mortality worldwide. In the United States, the prevalence of obesity is higher in African Americans than whites, even after adjustment for socioeconomic status (SES). This leads to the hypothesis that differences in genetic background may contribute to racial/ethnic differences in obesity-related traits. We tested this hypothesis by conducting a genome-wide admixture…
edyong | September 7, 2009The natural world is rife with leftovers. Over the course of evolution, body parts that no longer benefit their owners eventually waste, away leaving behind shrivelled and useless anatomical remnants. The human tailbone is one such example. Others include the sightless eyes of cavefish that live in total darkness, the tiny spurs on boas and pythons that hint at the legs of their ancestors, and the withered wings of the Galapagos cormorant, an animal that dispensed with flight on an island bereft of land predators.
Animal genomes contain similar remains. Just like organs, genes also waste…
razib | September 6, 2009I was doing some digging around on the genetics of Central Asia and stumbled upon the data that 7% of the mtDNA lineages of the Hui, Muslims who speak Chinese, are West Eurasian. This is opposed 0% for the Han, and 40-50% for the Uyghur. No surprises. But then I thought, what sort of exogamy rates would result in the Hui becoming, operationally, 90% Han during their stay in China? I think 10% is a conservative proportion for how much total genome content they have that is West Eurasian because the historical records suggest a male bias in the migration (so mtDNA would underestimate the…
razib | September 5, 2009Singapore is a racially diverse society, so there's a natural pool of diversity from which one can draw for study of human variation. The Han majority of Singapore derive predominantly from Fujian in southeast China. The Indians are mostly from the southern regions dominated by Tamils or Telugus, but there are large minorities from all over the subcontinent. Finally, the Malay category is really an amalgam of peoples of Southeast Asian Muslim origin, from native Singaporean Malays, to Malaysian Malays, to immigrants from Indonesia.
Singapore Genome Variation Project: A haplotype map of three…
razib | September 4, 2009After reading Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers I'm left scratching my head a bit. Cut-out black & white models really benefit from lack of data, and now that there's some serious data I think perhaps that we need to think about starting from a clean slate in many ways. The title of the article is rather justified in the local contexts: on the mitochondrial DNA (female lineage) there is an enormous difference between farming and non-farming populations. Here are the locations of these samples:
The genetic disance seems to have been 5-…
razib | September 4, 2009Dienekes posted some abstracts of the ASHG 2009 meeting. This one is in the category of facts we assumed but weren't totally sure of:
Abraham's children in the genome era: Major Jewish Diaspora populations comprise distinct genetic clusters with shared Middle Eastern ancestry
Here, we present population structure results from compiled datasets after merging with the Human Genome Diversity Project and the Population Reference Sample studies, which consisted of 146 non-Jewish Middle Easterners (Druze, Bedouin and Palestinian), 30 northern Africans (Mozabite from Algeria), 1547 Europeans, and…
razib | September 3, 2009Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers:
Following the domestication of animals and crops in the Near East some 11,000 years ago, farming reached much of Central Europe by 7,500 years before present. The extent to which these early European farmers were immigrants, or descendants of resident hunter-gatherers who had adopted farming, has been widely debated. We compare new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers, and from modern Europeans. We find large genetic differences…
razib | September 2, 2009Dan MacArthur has a very good post, New York Times adopts medical establishment line on personal genomics:
The NY Times has an article entitled "Buyer beware of home DNA tests" that adopts the paternalistic party line of the medical establishment: taking DNA tests without a doctor's advice is hazardous to your health.
Remarkably, the article acknowledges that qualified genetic counsellors are few and far between and that "most practicing physicians lack the knowledge and training in genetics to interpret [DNA tests] properly", and yet still suggests that customers should "take the findings to…
razib | September 1, 2009I have recently mentioned an analogy between the heritability of height & weight. That is, the proportion of variance of the trait which can be explained by variance in the genes. How closely do parents resemble offspring. A new paper in PLoS ONE, How Humans Differ from Other Animals in Their Levels of Morphological Variation, look at how this variation among human populations compares to other animals:
Animal species come in many shapes and sizes, as do the individuals and populations that make up each species. To us, humans might seem to show particularly high levels of morphological…