genetics
gregladen | June 22, 2008Continuing with our discussion of the Evolution 2008 conference, I was hoping to meet T. Ryan Gregory yesterday. He is listed on the Evolution 2008 program as an author of a talk on genome size. Goodnews/badnews: Gregory did not show, but the talk, given by his coauthor working in his lab, was excellent, so we didn't need him.
The research was done, and the paper delivered, by Jillian Smith. The title of the paper was "Genome size evolution in mammals" but it was more focused on specific results Jillian had come up with regarding bats.
source The bottom line is this: Genome size…
razib | June 21, 2008Comparing Genetic Ancestry and Self-Described Race in African Americans Born in the United States and in Africa (H/T Yann):
Genetic association studies can be used to identify factors that may contribute to disparities in disease evident across different racial and ethnic populations. However, such studies may not account for potential confounding if study populations are genetically heterogeneous. Racial and ethnic classifications have been used as proxies for genetic relatedness. We investigated genetic admixture and developed a questionnaire to explore variables used in constructing racial…
mikethemadbiologist | June 21, 2008
Gimme back my PAUP* menus!
One of the most unheralded breakthroughs in DNA sequence analysis--and, in particular, phylogenetics--was PAUP*. PAUP* is software that uses morphology or DNA sequence to construct phylogenies; that is, how organisms are related to another**.
Originally, PAUP* was only Mac compatible. The 4.0 version had all sorts of nice pull down menus and little buttons to click. Not only did this make it an exceptional teaching tool, but it was also easy to use. The Intel-Mac, PC, and Unix versions operate through a command line (and the documentation for the command line…
gregladen | June 20, 2008The Evolution 2008 conference started out today with a special program for K-12 teachers (mainly life science teachers) organized by the Minnesota Citizens for Science Education (MNCSE). The opening speaker was Scott Lanyon, director of the Bell Museum of Natural History. (The Bell hosted this event.)
Scott's objective was to outline several areas of evolutionary biology where fundamental changes had occurred over recent years. This was to provide perspective and food for thought for the Life Sciences teachers attending the event, and Scott was very successful in this effort.
In each case…
grrlscientist | June 19, 2008tags: researchblogging.org, phylogeny, British birds, population decline, range contraction, Gavin H Thomas
An adult male Eurasian blackbird, Turdus merula.
Image: Wikipedia commons [larger view].
A paper recently published by British scientist, Gavin Thomas, a population biologist at Imperial College London, finds that British bird species that currently are suffering population declines tend to be close relatives of each other. The reason is obvious: closely related species tend to share many traits, such as very precise habitat requirements, and what's bad for one species is also bad…
evolgen | June 18, 2008John Hawks has an interesting post on what it means to be human in which he argues that our "human-ness" (humanity?) is our shared evolutionary history. I like it. But Hawks also writes the following:
It is our history that connects us to our distant relatives, not our genes. Even with a close relative like a twentieth cousin, there is a decent likelihood that you will share no genes at all because of your shared kinship from your most recent common ancestor. By the fiftieth generation, it is a virtual certainty. You are a genetic stranger to your ancestors.
I could share no genes with my…
razib | June 16, 2008Genetic and Environmental Effects on Same-sex Sexual Behavior: A Population Study of Twins in Sweden:
There is still uncertainty about the relative importance of genes and environments on human sexual orientation. One reason is that previous studies employed self-selected, opportunistic, or small population-based samples. We used data from a truly population-based 2005-2006 survey of all adult twins (20-47 years) in Sweden to conduct the largest twin study of same-sex sexual behavior attempted so far. We performed biometric modeling with data on any and total number of lifetime same-sex…
edyong | June 16, 2008Jellyfish may seem like simple blobs of goo, but some are surprisingly sophisticated. The box jellyfish (Tripedelia cystophora), for example, is a fast and active hunter and stalks its prey with the aid of 24 fully functioning eyes. These are grouped into four clusters called rhopalia, which lie on each side of its cube-like body. Together, they give the box jellyfish a complete 360 degree view of its world and make it highly manoeuvrable.
Each eye cluster, four eyes are merely pits containing light-sensitive pigments, but two are remarkably advanced and carry their own lenses, retinas and…
edyong | June 14, 2008
We've all found gems hidden among junk before - the great album you own but never listened to, the book on your shelf that you never read, or the boot sale item that's worth a fortune. Geneticists are no different. Two years ago, Katherine Pollard and Sofie Salama discovered that one of the most important genes in human evolution has been lying in plain sight, hidden within a pile of genetic clutter.
Humans and our closest cousins, chimpanzees, evolved from a common ancestor, and we famously share anywhere from 96-99% of our DNA. This similarity suggests an obvious question: what are…
razib | June 13, 2008Via Dienekes, Ancient mtDNA from Sampula population in Xinjiang:
The archaeological site fo Sampula cemetery was located about 14âkm to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. 14C analysis showed that this cemetery was used from 217 B.C. to 283 A. D. Ancient DNA was analysed by 364âbp of the mitochondrial DNA hypervariable region 1 (mtDNA HVR-1), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of…
razib | June 12, 2008Over the past decade the concurrent arrival of relatively cheap sequencing technology as well as copious computational power has resulted a flurry of research in the domain of genetic anthropology with the intent of fleshing out historical questions. Spencer Wells' Journey of Man and Bryan Sykes' The Seven Daughters of Eve were among the early entrants in this burgeoning corpus of popular science literature. Both of these were relatively expansive works, focusing on the deep time histories of the Y and mtDNA lineages, the paternal and maternal ancestry respectively. As the low hanging…
razib | June 10, 2008This is cool, Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes:
We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by…
razib | June 6, 2008Notes on Sewall Wright: Population Size:
Continuing my series of notes on the work of Sewall Wright, I come to the question of population size. This is important in Wright's formulation of population genetics and his evolutionary theory generally. One of the major differences between Wright and R. A. Fisher is that Fisher believed that, in general, evolutionary processes could be treated as if they took place in a very large random-mating population. He did not believe, contrary to some caricatures, that species were literally random-mating across their entire range (which is obviously false…
razib | June 4, 2008You've probably read Carl and Ed's posts, but the paper is finally out, Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli:
The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000…
razib | June 3, 2008John Hawks has a post up, Handling exponential growth in demographic models. You might like to read it in concert with p-ter's post Modeling human demographic history. One question I have in regards to human evolutionary genetic history is this: how typical are our population dynamics up to this point for a typical sexually reproducing species? And therefore, how might that impact deviations for our species from the norm? Also, if you are interested in the intersection of evolutionary genetics and models of demography you can go back to R. A. Fisher's Genetical Theory of Natural…
razib | June 1, 2008I realized today that my post about doing quantitative genetic back-of-the-envelopes was rather wordy. And, I have a hunch that those who "got it" already have an intuitive feel for what I'm talking about, so I thought perhaps the easiest way to get people to develop a better feel was to roll up the calculations into a small Javascript calculator. You can find it below the fold. The terms are defined in the earlier post, but I plugged in the default values (you can change them if you want). Obviously you enter in inches or centimeters depending on whether you're normal or Canadian.…
razib | June 1, 2008I was chatting with a friend about a few quantitative genetic "back-of-the-envelopes." Specifically, about the expectation of the heights of the offspring of any given couple in the United States. I say the United States because it is a nation where most people get enough to eat; that means that heritability is on the order of 80-90% for this trait. By this, I mean that 80-90% of the variation in height we see within the population is due to variation in genetics. Those who are tall are likely to have tall parents, and those who are short are likely to have short parents. The key is…
edyong | June 1, 2008
You inherited your genes from your parents, half from your father and half from your mother. Almost all other animals contend with the same hand-me-down processes, but not the bdelloid rotifers. This intriguing group of small freshwater creatures are not content with their genetic hand-me-downs; they import genes too. A new study shows that their genomes are rife with legions of foreign DNA, transferred from bacteria, fungi and even plants.
The swapping of genetic material is all part of a day's activity for bacteria but it's incredibly rare in animals. But bdelloids are bringing in…
razib | May 31, 2008Haven't had a time to check this paper out, but looks real interesting, Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome:
Although mutations are known to cause varying degrees of harmful effects, it is difficult to quantify the distribution that best describes the variation of fitness effects of these mutations. Here we present a new method for inferring this distribution and inferring population history using Single Nucleotide Polymorphism (SNP) data from human populations. Using 47,576 SNPs discovered in 11,404 genes from sequencing 35 individuals (20 European…
razib | May 29, 2008Here's another example of how genetic methods can shed light on archaeological questions, Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland:
The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures is unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human, using 3400- to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq…