I've been keeping up a theme over the past week (here, here, here, here) on the climatic conditions during the major stages of human evolution. This seems like a realy important thing to know in order to understand the context and cause of hominin speciation events, and evolutionary change within hominin species. There is a paper in the latest issue of Evolutionary Anthropology reporting on a recent conference.
First off, we seem to have pretty good evidence that the earth's climate is quite heterogeneous over time. What are the implications of this for the "evolutionary histories of organisms"? There is a need to understand the link between climate variables and species turnover.
C. Lepre showed evidence that "African homo erectus originated during a period of precessional insolation and monsoon variability...rather than during a subsequent era of increased aridity"
The rest of the description illustrates how little we know about past climates. It seems that we just know a lot about how varaible the climate was. There were also discussions about new ways to measure past climatic conditions, most notably lake cores from various lakes in East Africa. The information gathered from these lake cores will have to be integrated with other fossil evidence.
"Finally, improved models are needed regarding how primates and other large mammals interact with food resources, competitors, predators, and disease vectors under changing rainfall and temperature regimes"
I know very little about climatology and I must say that I was dissapointed by how little I learned from this report. I think that this conference wasn't really about recapping current knowledge, but rather about discussing recent finds and discussing future research areas. I agree that it is important to think about how different climates affect ecologies (specifically human ecologies), thus affecting human biology, evolution etc...
Tuesday, February 27, 2007
Monday, February 26, 2007
Monday map - Great rift valley
I originally wanted to get a map of what this area would have looked like in the past... say 2 million years ago or 150, 000 years ago (more water, more and different vegetation?), but could not find that, so I'll just content myself with this map showing some of the major Australopithecus finds in the area.
One year anniversary of this blog
Well, it's been one year since my first post... so what do I have to say for myself? ..well I can say that I've learned quite a bit just by forcing myself to look at papers a little bit more closely so that I can post on them, although sometimes I just put up abstracts. I've noticed that I may spend a little bit more time that I probably should on the blog, thus taking away time from writing my dissertation.
I'm looking forward to many more years of learning new things and sharing them.
I'm looking forward to many more years of learning new things and sharing them.
MC1R SNPs and phenotype
- Determination of Phenotype Associated SNPs in the MC1R Gene
Branicki W, Brudnik U, Kupiec T, Wolanska-Nowak P, Wojas-Pelc A.
Abstract: Prediction of physical appearance based on genetic analysis is a very attractive prospect for forensic investigations. Recent studies have proved that there is a significant association between some genetic variants of the melanocortin 1 receptor (MC1R) gene and red hair color. The present study focuses on the potential forensic applicability of variation within this pigment-related gene. Sequencing of the complete MC1R gene was performed on a group of red-haired individuals and controls with different pigmentation. A major role in determination of red hair color is played by two MC1R variants-C451T and C478T. The optimized minisequencing assay for genotyping of the above positions and three other important red hair-related MC1R polymorphisms, C252A, G425A, and G880C was successfully applied to analyze typical forensic specimens. Determination of a homozygous or heterozygous combination can be a good predictor of both red hair color and fair skin of a subject.
Friday, February 23, 2007
Chimps make spears
A paper in Current Biology (see abstract below) reports on chimps that fashion spears and use them to get bush babies (small prosimians). The spears are made of branches that are slightly sharpened at the tip by knawing. It seems that they kind of poke and try to immobilize the bush babies in holes where they hide. They found this behavior to be most prevalent among females and immatures. This reminds me of a tv show I saw last night where captive male chimps did not attempt to make ketchup fishing tools nearly as much as females did. Is this because males are "too good" for this kind of "small time" food acquisition and are more interested in acquiring more substantial sources of food (hunting for monkeys)?
The authors make a case for the importance of studying these savannah chimpanzees living in Senegal, since they inhabit a environment similar to our EEA (environment of evolutionary adaptedness).
There are movies in the 'supplementary data" section.
Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools
Jill D. Pruetz, and Paco Bertolani
Current Biology, In press
Abstract: Although tool use is known to occur in species ranging from naked mole rats [1] to owls [2], chimpanzees are the most accomplished tool users [3, 4, 5]. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these. Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.
The authors make a case for the importance of studying these savannah chimpanzees living in Senegal, since they inhabit a environment similar to our EEA (environment of evolutionary adaptedness).
There are movies in the 'supplementary data" section.
Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools
Jill D. Pruetz, and Paco Bertolani
Current Biology, In press
Abstract: Although tool use is known to occur in species ranging from naked mole rats [1] to owls [2], chimpanzees are the most accomplished tool users [3, 4, 5]. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these. Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.
Thursday, February 22, 2007
Jablonksi on birth rate, competition, and hominid extinctions
I don't know how this happened, but ever since my monday map on the ice age, I've run across several papers or reports discussing or mentioning the ice age...here's another:
via the TAMU Anthro in the News, there's this writeup called "Birth rate, competition are major players in hominid extinctions" about a talk by Nina Jablonki at the AAAS meetings.
some of the more interesting excerpts:
Primates evolved in the Paleocene and Eocene when worldwide climate was less seasonal. The beneficial environment allowed primates to evolve as relatively brainy animals that reproduce slowly. However, when climate changed so that tropical forests shrunk and the environment became patchy, many species including primate species became extinct.
"We find that the early members of the genus Homo who succeeded were super ecological opportunists," says Jablonski. "They would eat vegetation and scavenge, kill small animals and forage."
regarding Neanderthals:
Leading up to and during the last glacial maximum about 18,000 years ago, the grassy plains disappeared, taking with them the animals that relied on large expanses of grass for grazing. These animals were the prime food source for Neandertal...
At the same time, modern Homo sapiens experienced the same reduction in large animal game, but switched to also fishing, snaring small mammals like rabbits and capturing turtles and birds.
via the TAMU Anthro in the News, there's this writeup called "Birth rate, competition are major players in hominid extinctions" about a talk by Nina Jablonki at the AAAS meetings.
some of the more interesting excerpts:
Primates evolved in the Paleocene and Eocene when worldwide climate was less seasonal. The beneficial environment allowed primates to evolve as relatively brainy animals that reproduce slowly. However, when climate changed so that tropical forests shrunk and the environment became patchy, many species including primate species became extinct.
"We find that the early members of the genus Homo who succeeded were super ecological opportunists," says Jablonski. "They would eat vegetation and scavenge, kill small animals and forage."
regarding Neanderthals:
Leading up to and during the last glacial maximum about 18,000 years ago, the grassy plains disappeared, taking with them the animals that relied on large expanses of grass for grazing. These animals were the prime food source for Neandertal...
At the same time, modern Homo sapiens experienced the same reduction in large animal game, but switched to also fishing, snaring small mammals like rabbits and capturing turtles and birds.
"Rather than being a specialized large mammal predator, modern humans would eat anything they could get their hands on. They eked out a living even if it meant eating grasshoppers or whatever," says Jablonski. "Even with this, modern humans barely hung on from 12 to 16,000 years ago.
"Why did Neandertal not adapt culturally?" she asks. "Why did they not start eating bunnies? They did begin fishing."
Jablonski believes that competition from modern humans was already too strong. The environment was marginal and modern humans were already foraging and small-animal collecting.
"I think they were out-competed at the very end," says Jablonski. "Modern humans simply did it better, more nimbly."
A lot of this contradicts what was said in the paper I posted on a couple of days ago said, notably that moderns had projectile technology that allowed them to hunt big game more efficiently than Neanderthals.
Wednesday, February 21, 2007
More on the ice age - Neanderthal extinction by "freezing"
There's a BBC story about a new paper out that proposes that Neanderthals were killed off by cold climate about 24,000 years ago. This seems to correspond to when the climate was the coldest in Europe during the last ice age.
Phenotypic plasticity in Drosophila pigmentation
Thank goodness for model organisms like drosophila, mice, zebrafish etc... Without them, it would be much harder to understand the molecular nuts and bolts of genes and phenotypes.
I recently went over phenotypic plasticity in my intro to bioanthro class, so I thought I would post this new paper here. I also did a related (but much much much much simpler) project in high school on circadian rhythm regulated plasticity in fiddler crab pigmentation.
Phenotypic Plasticity in Drosophila Pigmentation Caused by Temperature Sensitivity of a Chromatin Regulator Network.
Gibert JM, Peronnet F, Schlotterer C.
PLoS Genetics 2007 Feb 16;3(2):e30
Abstract: Phenotypic plasticity is the ability of a genotype to produce contrasting phenotypes in different environments. Although many examples have been described, the responsible mechanisms are poorly understood. In particular, it is not clear how phenotypic plasticity is related to buffering, the maintenance of a constant phenotype against genetic or environmental variation. We investigate here the genetic basis of a particularly well described plastic phenotype: the abdominal pigmentation in female Drosophila melanogaster. Cold temperature induces a dark pigmentation, in particular in posterior segments, while higher temperature has the opposite effect. We show that the homeotic gene Abdominal-B (Abd-B) has a major role in the plasticity of pigmentation in the abdomen. Abd-B plays opposite roles on melanin production through the regulation of several pigmentation enzymes. This makes the control of pigmentation very unstable in the posterior abdomen, and we show that the relative spatio-temporal expression of limiting pigmentation enzymes in this region of the body is thermosensitive. Temperature acts on melanin production by modulating a chromatin regulator network, interacting genetically with the transcription factor bric-a-brac (bab), a target of Abd-B and Hsp83, encoding the chaperone Hsp90. Genetic disruption of this chromatin regulator network increases the effect of temperature and the instability of the pigmentation pattern in the posterior abdomen. Colocalizations on polytene chromosomes suggest that BAB and these chromatin regulators cooperate in the regulation of many targets, including several pigmentation enzymes. We show that they are also involved in sex comb development in males and that genetic destabilization of this network is also strongly modulated by temperature for this phenotype. Thus, we propose that phenotypic plasticity of pigmentation is a side effect reflecting a global impact of temperature on epigenetic mechanisms. Furthermore, the thermosensitivity of this network may be related to the high evolvability of several secondary sexual characters in the genus Drosophila.
I recently went over phenotypic plasticity in my intro to bioanthro class, so I thought I would post this new paper here. I also did a related (but much much much much simpler) project in high school on circadian rhythm regulated plasticity in fiddler crab pigmentation.
Phenotypic Plasticity in Drosophila Pigmentation Caused by Temperature Sensitivity of a Chromatin Regulator Network.
Gibert JM, Peronnet F, Schlotterer C.
PLoS Genetics 2007 Feb 16;3(2):e30
Abstract: Phenotypic plasticity is the ability of a genotype to produce contrasting phenotypes in different environments. Although many examples have been described, the responsible mechanisms are poorly understood. In particular, it is not clear how phenotypic plasticity is related to buffering, the maintenance of a constant phenotype against genetic or environmental variation. We investigate here the genetic basis of a particularly well described plastic phenotype: the abdominal pigmentation in female Drosophila melanogaster. Cold temperature induces a dark pigmentation, in particular in posterior segments, while higher temperature has the opposite effect. We show that the homeotic gene Abdominal-B (Abd-B) has a major role in the plasticity of pigmentation in the abdomen. Abd-B plays opposite roles on melanin production through the regulation of several pigmentation enzymes. This makes the control of pigmentation very unstable in the posterior abdomen, and we show that the relative spatio-temporal expression of limiting pigmentation enzymes in this region of the body is thermosensitive. Temperature acts on melanin production by modulating a chromatin regulator network, interacting genetically with the transcription factor bric-a-brac (bab), a target of Abd-B and Hsp83, encoding the chaperone Hsp90. Genetic disruption of this chromatin regulator network increases the effect of temperature and the instability of the pigmentation pattern in the posterior abdomen. Colocalizations on polytene chromosomes suggest that BAB and these chromatin regulators cooperate in the regulation of many targets, including several pigmentation enzymes. We show that they are also involved in sex comb development in males and that genetic destabilization of this network is also strongly modulated by temperature for this phenotype. Thus, we propose that phenotypic plasticity of pigmentation is a side effect reflecting a global impact of temperature on epigenetic mechanisms. Furthermore, the thermosensitivity of this network may be related to the high evolvability of several secondary sexual characters in the genus Drosophila.
Monday, February 19, 2007
Ice age ecology and neanderthals vs. moderns
Speaking of the ice age, I happened to run across this new review paper that has some great illustrations, but I'm not sure what to make of what they're tryng to say (probably due to the lack of my background knowledge in this area). One thing that struck me was the following passage:"Open woodland (e.g. red deer Cervus elaphus) and rocky habitat (e.g. ibex Capra ibex) mammalian herbivores offered opportunities for human ambush hunters [5]. Humans with projectile technology and long-range mobility, which enabled the following of the large herds, were best suited to exploiting plains mammals (e.g. horse, Equus ferus, reindeer Rangifer tarandus and steppe bison Bison priscus) [5]. The expansion of plains mammals across the Palaearctic as treeless vegetation spread 37 and 39 was a crucial factor in the fate of human populations. It favoured the AMHs and constrained the Neanderthals [5]."
Rapid ecological turnover and its impact on Neanderthal and other human populations
Clive Finlayson, Jose Carrion
Trends in Ecology and Evolution Article inPress
Abstract: The latter part of the last glaciation, 50 000–12 000 years ago (kya), was characterized by a rapidly changing climate, cold conditions and corresponding vegetation and faunal turnover. It also coincided with the extinction of the Neanderthals and the expansion of modern human populations. Established views of modern human superiority over Neanderthals as the cause of their extinction are under attack as recent work shows that Neanderthals were capable of behaviour that is regarded as modern. As we discuss here, the exact nature of biological and cultural interactions between Neanderthals and other human groups between 50 kya and 30 kya is currently hotly contested. The extinction of the Neanderthals, and other modern human lineages, now appears to have been a drawn-out, climate-related affair.
Monday Map - Ice Age
I'm not sure where I'm going with this one, but I was just thinking about the climatic conditions during the time humans went into Eurasia and the Americas...it must have been cold.. (much?) colder than it is now. The last ice age seemed to have lasted from about 125,000 years ago to about 20,000 years ago (when it was coldest). Since then, it seems to have warmed up very quickly. This is interesting to think about in terms of recent selection, population differences, strength of selection for skin color etc... Has this selection been relaxed in the last 20,000 years due to the rewarming?
Saturday, February 17, 2007
One variant of TYRP1 controls all coat color variation in sheep
According to this paper, a variant in TYRP1 controls most, if not all the variation in coat color in Soay sheep...this is pretty cool because this gene is one of the handful that is known to influence skin color in humans (albinism) and several animals, and has been shown to be under positive selection (Voight PloS paper and recent AHG Lao paper, via Dienenkes) in humans....also see this post and Razib's corresponding post. The color of these sheep (see pictures) remind me of human skin color variation.
Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep
J. Gratten, D. Beraldi, B.V. Lowder, A.F. McRae, P.M. Visscher, J.M. Pemberton, J. Slate
Proceedings of the Royal Society B: Biological Sciences Volume 274, Number 1610 / March 07, 2007 Pages: 619 - 626
Abstract: Identifying the genes that underlie phenotypic variation in natural populations is a central objective of evolutionary genetics. Here, we report the identification of the gene and causal mutation underlying coat colour variation in a free-living population of Soay sheep (Ovis aries). We targeted tyrosinase-related protein 1 (TYRP1), a positional candidate gene based on previous work that mapped the Coat colour locus to an approximately 15cM window on chromosome 2. We identified a non-synonymous substitution in exon IV that was perfectly associated with coat colour. This polymorphism is predicted to cause the loss of a cysteine residue that is highly evolutionarily conserved and likely to be of functional significance. We eliminated the possibility that this association is due to the presence of strong linkage disequilibrium with an unknown regulatory mutation by demonstrating that there is no difference in relative TYRP1 expression between colour morphs. Analysis of this putative causal mutation in a complex pedigree of more than 500 sheep revealed almost perfect co-segregation with coat colour (χ2-test, p<0.0001, lod="110.20)," lod="29.50).
Thursday, February 15, 2007
Peopling of the Americas
check out kambiz's post at Anthropology.net on a forthcoming paper about a polymorphism found in "all" Native American populations and only in two populations of Siberians in the Asian northeast. This could mean (or not mean) a lot of things, and you can't really draw many conlusions from this, but I suppose it does lend further support to the idea that Native Americans and northeastern (asia) Siberians shared a recent common ancestor. Is this anything really new?.. and it's just one marker... Actually, I'm not really familiar with the background research on this issue of Native American/Asian/Siberian population genetics so I shouldn't say too much. I guess the competing hypothesis here is that NA could trace some of their ancestry to other Asian populations.
Tuesday, February 13, 2007
Rates of evolution in brain-expressed genes
The discussion section of this paper does a good job of presenting different and interesting ways of interpreting what they find - why human brain-expressed genes have evolved slowly.
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates
Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, Chen-Kung Chou, Shih-Feng Tsai, Chung-I Wu, C.-K. James Shen
PLoS Biology 5(2): e13
Abstract: Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) and then conducted three-way comparisons among (i) mouse, OWM, and human, and (ii) OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes > OWM > mouse), a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal) in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-à-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i) faster evolution in gene expression, and (ii) a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed.
Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates
Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, Chen-Kung Chou, Shih-Feng Tsai, Chung-I Wu, C.-K. James Shen
PLoS Biology 5(2): e13
Abstract: Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) and then conducted three-way comparisons among (i) mouse, OWM, and human, and (ii) OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes > OWM > mouse), a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal) in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-à-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i) faster evolution in gene expression, and (ii) a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed.
Monday, February 12, 2007
Monday Map
From the International Satellite Cloud Climatology Project, this map shows the average annual cloud cover around the world. I thought it would be interesting to combine this data along with insolation data to look for any population skin color anomalies. Unfortunately, I don't have time to look at this very closely right now, although I'll just point out that Jared Diamond frequently mentions the example of dark skin color in Papua New Guinea despite much cloud cover...
Sunday, February 11, 2007
European genetic substructure
Dienekes has a post on a new AJHG paper by Marc Bauchet, Mark Shriver and others on European substructure. Dienekes covers it pretty well, including the picture of the Structure output of K=2 to K=6.
This study looks at 297 people from Europe with 10,000 SNPs
Like this previous study by Seldin et al. , the Finns are more in the fuzzy area of the Europe-Asia gradient (or just off on their own).
Surprisingly with 10,000 SNPs, it seems to be hard to resolve much substructure in Europe - the yellow part of the Structure picture is not broken up much, except for the Finns and the Southeast Europeans. The sample sizes from each country are quite small (about 10 per country).
They do provide a list of SNPs that are especially informative for distinguishing northern from southern Europeans.
This study looks at 297 people from Europe with 10,000 SNPs
Like this previous study by Seldin et al. , the Finns are more in the fuzzy area of the Europe-Asia gradient (or just off on their own).
Surprisingly with 10,000 SNPs, it seems to be hard to resolve much substructure in Europe - the yellow part of the Structure picture is not broken up much, except for the Finns and the Southeast Europeans. The sample sizes from each country are quite small (about 10 per country).
They do provide a list of SNPs that are especially informative for distinguishing northern from southern Europeans.
Saturday, February 10, 2007
Good brain function and Schizophrenia - antagonisitc pleiotropy?
Genetic evidence implicating DARPP-32 in human frontostriatal structure, function, and cognition
Andreas Meyer-Lindenberg, Richard E. Straub, Barbara K. Lipska, Beth A. Verchinski, Terry Goldberg, Joseph H. Callicott, Michael F. Egan, Stephen S. Huffaker, Venkata S. Mattay, Bhaskar Kolachana, Joel E. Kleinman and Daniel R. Weinberger
J. Clin. Invest. Published online Feb 8, 2007
Abstract: Dopamine- and cAMP-regulated phosphoprotein of molecular weight 32 kDa (DARPP-32), encoded by PPP1R1B, is a pivotal integrator of information in dopaminoceptive neurons, regulating the response to neuroleptics, psychotomimetics, and drugs of abuse, and affecting striatal function and plasticity. Despite extensive preclinical work, there are almost no data on DARPP-32 function in humans. Here, we identify, through resequencing in 298 chromosomes, a frequent PPP1R1B haplotype predicting mRNA expression of PPP1R1B isoforms in postmortem human brain. This haplotype was associated with enhanced performance on several cognitive tests that depend on frontostriatal function. Multimodal imaging of healthy subjects revealed an impact of the haplotype on neostriatal volume, activation, and the functional connectivity of the prefrontal cortex. The haplotype was associated with the risk for schizophrenia in 1 family-based association analysis. Our convergent results identify a prefrontal-neostriatal system affected by variation in PPP1R1B and suggest that DARPP-32 plays a pivotal role in cognitive function and possibly in the pathogenesis of schizophrenia.
Friday, February 09, 2007
SNPs and CNVs affect gene expression, with little overlap
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
Barbara E. Stranger, Matthew S. Forrest, Mark Dunning, Catherine E. Ingle, Claude Beazley, Natalie Thorne Richard Redon, Christine P. Bird, Anna de Grassi, Charles Lee, Chris Tyler-Smith, Nigel Carter, Stephen W. Scherer, Simon Tavaré, Panagiotis Deloukas, Matthew E. Hurles, Emmanouil T. Dermitzakis
Science 9 February 2007:Vol. 315. no. 5813, pp. 848 - 853
Abstract: Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely, single-nucleotide polymorphisms (SNPs). In recent years, another type of common genetic variation has been characterized, namely, structural variation, including copy number variants (CNVs). To determine the overall contribution of CNVs to complex phenotypes, we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans.
Barbara E. Stranger, Matthew S. Forrest, Mark Dunning, Catherine E. Ingle, Claude Beazley, Natalie Thorne Richard Redon, Christine P. Bird, Anna de Grassi, Charles Lee, Chris Tyler-Smith, Nigel Carter, Stephen W. Scherer, Simon Tavaré, Panagiotis Deloukas, Matthew E. Hurles, Emmanouil T. Dermitzakis
Science 9 February 2007:Vol. 315. no. 5813, pp. 848 - 853
Abstract: Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely, single-nucleotide polymorphisms (SNPs). In recent years, another type of common genetic variation has been characterized, namely, structural variation, including copy number variants (CNVs). To determine the overall contribution of CNVs to complex phenotypes, we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans.
Wednesday, February 07, 2007
Polar populations in AJHB
The American Journal of Human Biology's newest issue looks like a special issue on circumpolar populations (although this is never explicitly mentioned anywhere on the website). This journal consistently has research that I find immensely interesting, and this issue is no exception. Unfortunately, I don't get full-text access (shame on my university), which makes it a bit harder (although not impossible) to read... life is tough.As someone who is interested in human biodiversity, adaptation to cold environments is something that I consider to be very important.
This issue has papers reviewing health risks among Inuit, including one by T.K. Young that discusses the need for "ethnospecific obesity criteria" as the Inuit fit most of the criteria for obesity but "the "dose-response" curves for the impact of obesity on metabolic indicators such as plasma lipids and blood pressure are lower than in other populations." There's also a paper by M. Crawford on the genetic structure of circumpolar populations, and a paper on "Human cold exposure, adaptation, and performance in high latitude environments" by Tiina Makinen.Right on, AJHB!!
MC1R allele frequencies
Comprehensive evaluation of allele frequency differences of MC1R variants across populations.
Gerstenblith MR, Goldstein AM, Fargnoli MC, Peris K, Landi MT.
Hum Mutat. 2007 Feb 5; [Epub ahead of print]
Abstract: The melanocortin 1 receptor (MC1R), a member of the G protein-coupled receptors superfamily, mediates the response to melanocortins and is currently the best-described contributor to normal pigment variation in humans. A remarkably large number of natural polymorphisms, or variants, of the MC1R gene have been identified in different populations. Some of these variants have been associated with specific hair and skin color phenotypes, the presence of freckling, and melanoma and nonmelanoma skin cancer risk. Interestingly, some MC1R variants have been associated with skin cancer beyond their effects on pigmentation. Although the red hair color variants (RHC variants) have been associated with skin cancer risk in the Celtic population, studies in darkly-pigmented Caucasian populations have demonstrated the importance of non-RHC MC1R variants on skin cancer risk as well. We have reviewed and compared allele frequency differences of MC1R variants across geographic regions. We observed large differences in the distribution of variants across populations, with a prominent difference between lightly and darkly-pigmented individuals. Moreover, among Caucasian groups, there were seven variants (p.V60L, p.V92M, p.D84E, p.R151C, p.R160W, p.R163Q, and p.D294H) with significantly different allele frequencies. Exploring differences in allele frequencies of MC1R variants across populations with varying pigmentation and differing skin cancer risk may improve our understanding of the complex relationship between MC1R, pigmentation, and carcinogenesis.
Gerstenblith MR, Goldstein AM, Fargnoli MC, Peris K, Landi MT.
Hum Mutat. 2007 Feb 5; [Epub ahead of print]
Abstract: The melanocortin 1 receptor (MC1R), a member of the G protein-coupled receptors superfamily, mediates the response to melanocortins and is currently the best-described contributor to normal pigment variation in humans. A remarkably large number of natural polymorphisms, or variants, of the MC1R gene have been identified in different populations. Some of these variants have been associated with specific hair and skin color phenotypes, the presence of freckling, and melanoma and nonmelanoma skin cancer risk. Interestingly, some MC1R variants have been associated with skin cancer beyond their effects on pigmentation. Although the red hair color variants (RHC variants) have been associated with skin cancer risk in the Celtic population, studies in darkly-pigmented Caucasian populations have demonstrated the importance of non-RHC MC1R variants on skin cancer risk as well. We have reviewed and compared allele frequency differences of MC1R variants across geographic regions. We observed large differences in the distribution of variants across populations, with a prominent difference between lightly and darkly-pigmented individuals. Moreover, among Caucasian groups, there were seven variants (p.V60L, p.V92M, p.D84E, p.R151C, p.R160W, p.R163Q, and p.D294H) with significantly different allele frequencies. Exploring differences in allele frequencies of MC1R variants across populations with varying pigmentation and differing skin cancer risk may improve our understanding of the complex relationship between MC1R, pigmentation, and carcinogenesis.
Basque differentiation
Polymorphic Alu insertions and the genetic structure of Iberian Basques.- Garcia-Obregon S, Alfonso-Sanchez MA, Perez-Miranda AM, de Pancorbo MM, Pena JA.
- Abstract: Eight Alu sequences (ACE, TPA25, PV92, APO, FXIIIB, D1, A25 and B65) were analyzed in two samples from Navarre and Guipuzcoa provinces (Basque Country, Spain). Alu data for other European, Caucasus and North African populations were compiled from the literature for comparison purposes to assess the genetic relationships of the Basques in a broader geographic context. Results of both MDS plot and AMOVA revealed spatial heterogeneity among these three population clusters clearly defined by geography. On the contrary, no substantial genetic heterogeneity was found between the Basque samples, or between Basques and other Europeans (excluding Caucasus populations). Moreover, the genetic information obtained from Alu data conflicts with hypotheses linking the origin of Basques with populations from North Africa (Berbers) or from the Caucasus region (Georgia). In order to explain the reduced genetic heterogeneity detected by Alu insertions among Basque subpopulations, values of the Wright's F(ST )statistic were estimated for both Alu markers and a set of short tandem repeats (STRs) in terms of two geographical scales: (1) the Basque Country, (2) Europe (including Basques). In the Basque area, estimates of Wahlund's effect for both genetic markers showed no statistical difference between Basque subpopulations. However, when this analysis was performed on a European scale, F(ST) values were significantly higher for Alu insertions than for STR alleles. From these results, we suggest that the spatial heterogeneity of the Basque gene pool identified in previous polymorphism studies is relatively recent and probably caused by a differential process of genetic admixture with non-Basque neighboring populations modulated by the effect of a linguistic barrier to random mating.
Tuesday, February 06, 2007
New Alan Rogers et al. paper out on "Ancestral Alleles and Population origins..."
Dienekes posted on this new paper a few days ago. It looks important and interesting, and I've been meaning to read it, but just haven't gotten around to it. According to Dienekes and from what I can glean from the abstract, it seems to challenge the recent common African origin of modern humans. (i.e. a LOT of introgression from archaics??)
Monday, February 05, 2007
Monday Map
Check out Worldmapper for hundreds of maps that shrink or inflate countries according to the category. Many of the maps show obvious, expected trends, and none really surprised me that much. What did surprise me was the fact that India and China were very often "inflated", probably due to a large population in a relatively small area. This map below shows diabetes prevalence (" Territory size shows the proportion of all people over 15 in the world living with diabetes who live there.")
Sunday, February 04, 2007
Diabetes, Mitochondria, Asians, adaptation to cold
This paper (see below) makes some interesting connections between diabetes related phenotyes, the role of mitochondria, and selection for adaptation to the cold. I don't quite "get it".
an excerpt from the conclusion:
Mitochondrial haplogroup N9a has a great diversity in the whole of China and Korea. In Japan, this haplogroup was not detected in aboriginal Ainu and Ryukyuans but only in mainland Honshu Japanese. This distribution suggests that this haplogroup was derived from the new immigrant, or Yayoi, people. These so-called mammoth hunters who had adapted to extremely cold climates in Siberia migrated back to the northern part of China 
According to the Wallace theory, adaptation to a cold climate might involve uncoupling of electron transfer with ATP production, to increase heat production.15,16 Thus, increased mitochondrial respiration and energy expenditure is essential to meet the ATP requirement. Such an uncoupling phenotype would be protective against the development of obesity and, consequently, T2DM. However, at present, we do not have evidence that N9a is associated with lean body status. Alternatively, the uncoupling phenotype might be related to decreased mitochondrial oxidative stress, which might in turn exert a protective effect against T2DM. Further functional analysis of cybrids carrying haplogroup N9a will be necessary to verify these hypotheses.
Mitochondrial Haplogroup N9a Confers Resistance against Type 2 Diabetes in Asians
Am. J. Hum. Genet., 80:407-415, 2007
Abstract: Because mitochondria play pivotal roles in both insulin secretion from the pancreatic cells and insulin resistance of skeletal muscles, we performed a large-scale association study to identify mitochondrial haplogroups that may confer resistance against or susceptibility to type 2 diabetes mellitus (T2DM). The study population comprised 2,906 unrelated Japanese individuals, including 1,289 patients with T2DM and 1,617 controls, and 1,365 unrelated Korean individuals, including 732 patients with T2DM and 633 controls. The genotypes for 25 polymorphisms in the coding region of the mitochondrial genome were determined, and the haplotypes were classified into 10 major haplogroups (i.e., F, B, A, N9a, M7a, M7b, G, D4a, D4b, and D5). Multivariate logistic-regression analysis with adjustment for age and sex revealed that the mitochondrial haplogroup N9a was significantly associated with resistance against T2DM (P = .0002) with an odds ratio of 0.55 (95% confidence interval 0.40–0.75). Even in the modern environment, which is often characterized by satiety and physical inactivity, this haplogroup might confer resistance against T2DM.
Arguments FOR "Aquatic ape"
From a fellow graduate student, check out this story at BBC on "The role of floods in ape evolution". I'm not familiar with all the counterarguments, but this is pretty compelling. I did post one very recent counterargument against "Aquatic Ape" here.
Friday, February 02, 2007
"Breast Tumors: More common in Whites, deadlier in Blacks"
This is a news feature in the new issue of Science profiling a female Nigerian doctor who is investigating the racial disparity in the aggressiveness of breast tumors.
Probing the Roots of Race and Cancer
Jennifer Couzin
Science 2 February 2007 Vol. 315. no. 5812, pp. 592 - 594
CHICAGO, ILLINOIS--African-American women are more likely to develop aggressive breast tumors than are Caucasians. Funmi Olopade is trying to understand why.
Some of the more interesting excerpts:
"She recently reported that even when black women with breast cancer receive the same treatment as whites in clinical trials, their chance of developing incurable metastases is about 20% greater."
"Her efforts intensified after tumor samples she collected 3 years ago from women in Nigeria and Senegal revealed an even higher rate of aggressive disease than in African-American women--suggesting that genetics may partly explain the difference."
"Many of the young black women in her clinic who had not inherited BRCA mutations, Olopade noticed, nonetheless seemed to develop a form of breast cancer that closely resembled that seen in BRCA1 carriers. Known as estrogen-receptor-negative (ER-negative) breast cancer, these tumors are not fueled by estrogen and do not respond to drugs such as tamoxifen and raloxifene that cut off their supply of the hormone. They also tend to metastasize and spread more quickly than ER-positive tumors."... "Nearly 40% of breast cancer cases among African-American women are ER-negative, compared with 23% of cases among whites."
and this last interesting snippet:
"In the Chicago health-disparity center to which Olopade devotes a slice of her time, another environmental driver may be emerging. Co-Director McClintock has shown that when rats are socially isolated early in life, increasing stress and vigilance and prompting immune system changes, they develop breast tumors 40% earlier and four times more often than do animals housed in groups. The isolated rats also display larger, more aggressive tumors."
Probing the Roots of Race and Cancer
Jennifer Couzin
Science 2 February 2007 Vol. 315. no. 5812, pp. 592 - 594
CHICAGO, ILLINOIS--African-American women are more likely to develop aggressive breast tumors than are Caucasians. Funmi Olopade is trying to understand why.
Some of the more interesting excerpts:
"She recently reported that even when black women with breast cancer receive the same treatment as whites in clinical trials, their chance of developing incurable metastases is about 20% greater."
"Her efforts intensified after tumor samples she collected 3 years ago from women in Nigeria and Senegal revealed an even higher rate of aggressive disease than in African-American women--suggesting that genetics may partly explain the difference."
"Many of the young black women in her clinic who had not inherited BRCA mutations, Olopade noticed, nonetheless seemed to develop a form of breast cancer that closely resembled that seen in BRCA1 carriers. Known as estrogen-receptor-negative (ER-negative) breast cancer, these tumors are not fueled by estrogen and do not respond to drugs such as tamoxifen and raloxifene that cut off their supply of the hormone. They also tend to metastasize and spread more quickly than ER-positive tumors."... "Nearly 40% of breast cancer cases among African-American women are ER-negative, compared with 23% of cases among whites."
and this last interesting snippet:
"In the Chicago health-disparity center to which Olopade devotes a slice of her time, another environmental driver may be emerging. Co-Director McClintock has shown that when rats are socially isolated early in life, increasing stress and vigilance and prompting immune system changes, they develop breast tumors 40% earlier and four times more often than do animals housed in groups. The isolated rats also display larger, more aggressive tumors."
Thursday, February 01, 2007
Four Stone Hearth 8
Four Stone Hearth 8, the Anthropology blog carnival is up at Northstate Science. Check it out for the latest in Anthropology blogging
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