Vitamin D deficiency in people with dark skin in the Netherlands

High prevalence of vitamin D deficiency in newborn infants of high-risk mothers.

Dijkstra SH, van Beek A, Janssen JW, de Vleeschouwer LH, Huysman WA, van den Akker EL.

Arch Dis Child. 2007 Sep;92(9):750-3

OBJECTIVE: To determine the prevalence of vitamin D deficiency in newborn infants of mothers at risk of vitamin D deficiency because of dark skin or the wearing of concealing clothes (such as a veil) compared with a group presumed not to be at risk. A second aim was to correlate these newborn infants' vitamin D concentrations with biochemical parameters of vitamin D metabolism and bone turnover at birth. DESIGN: A prospective study conducted between April 2004 and February 2006 including women delivering during this period and their newborn infants. SETTING: The outpatient clinic of the obstetrics department, Sint Franciscus Gasthuis, Rotterdam, the Netherlands. PATIENTS: Eighty seven newborn infants of healthy mothers with either dark skin and/or concealing clothing (risk group) or light skin (control group). RESULTS: We found a significant difference in the prevalence of vitamin D deficiency (25-hydroxyvitamin D(3) less than 25 nmol/l) between newborn infants of mothers at risk and those of mothers in the control group (63.3% vs 15.8%; p less than 0.001). Mean alkaline phosphatase concentrations were significantly higher in the at risk group. CONCLUSIONS: Newborn infants of mothers with dark skin or wearing concealing clothes are at great risk of vitamin D deficiency at birth. The clinical implications are unknown. Further research is necessary to determine the long-term consequences of maternal and neonatal vitamin D deficiency so that guidelines on vitamin D supplementation during pregnancy can be issued.

Flores hobbit is not a modern human?

A paper describing the wrist bone of the Flores individual supposedly shows more similarities with African apes and early hominins than with modern humans. This is going to come out in Science soon, so I'm just going on this Yahoo! News story.
we'll see how far this twist in the story goes...

Population genetics and demographics of Argentina

this study makes use of a combination of demographic/genealogical data with genetic data...

How many populations set foot through the Patagonian door? Genetic composition of the current population of Bahía Blanca (Argentina) based on data from 19 Alu polymorphisms.

Resano M, Esteban E, González-Pérez E, Vía M, Athanasiadis G, Avena S, Goicoechea A, Bartomioli M, Fernández V, Cabrera A, Dejean C, Carnese F, Moral P.
Am J Hum Biol. 2007 Sep 17; [Epub ahead of print]

Abstract: The city of Bahía Blanca occupies a strategic place in Argentina south of the Pampean region in the north-east corner of the Patagonia. Since 1828, this city has been the historical and political border between Amerindian lands in the south, and the lands of European colonists. Nowadays, Bahía Blanca is an urban population mainly composed by descendents of immigrants from Spain and other European countries with apparently low admixture with Amerindians. In view of the unexpectedly high Amerindian admixture levels (about 46.7%) suggested by mtDNA data, and protein markers (19.5%), we analyzed a set of 19 Alu polymorphisms (18 autosomal, 1 of Chromosome Y) in a well-documented genealogical sample from Bahía Blanca. The genotyped sample was made up of 119 unrelated healthy individuals whose birth place and grandparent origins were fully documented. According to available genealogical records, the total sample has been subdivided into two groups: Bahía Blanca Original (64 individuals with all 4 gandparents born in Argentina) and Bahía Blanca Mix (55 individuals with one to three grandparents born out of Argentina). Allele frequencies and gene diversity values in Bahía Blanca fit well into the European ranges. Population relationships have been tested for 8 Alu markers, whose variation has been described in several Amerindian and European samples. Reynolds genetic distances underline the significant genetic similarity of Bahía Blanca to Europeans (mean distance 0.044) and their differentiation from Amerindians (0.146). Interestingly enough, when the general sample is divided, Bahía Blanca Original appears slightly closer to Amerindians (0.127) in contrast to Bahía Blanca Mix (0.161). Furthermore, the genetic relationships depicted through a principal components analysis emphasize the relative similarity of Bahía Blanca Original to Amerindians. A thorough knowledge of the sample origins has allowed us to make a subtle distinction of the genetic composition of Bahía Blanca.

More on persistence/endurance hunting/running

The last post on endurance running/persistence hunting as an important human adaptation generated a lot of interest, so I thought I'd give an update. The new issue of Journal of Human Evolution has some commentaries between the authors of that paper and some critics of the idea.

The evolution of endurance running and the tyranny of ethnography: A reply to Pickering and Bunn (2007)

The endurance running hypothesis and hunting and scavenging in savanna-woodlands Travis Rayne Pickering, and Henry T. Bunn

In a nutshell, the critics cite paleo-environment evidence that Homo was in a denser savannah woodland enivronment two million years ago, that would not have been suitable for running long distances due to excessive vegetation and compact ground (as opposed to sand that would tire prey out). They also discuss the lack of any evidence for ER among Hadza and other groups, and the plausibility of sophisticated tracking abilities needed for ER hunting that far back (2mya). I'd have to say that I am pretty skeptical myself of the ER running hypothesis as a significant human adaptation. However I am not familiar enough with the physiological and anatomical evidence that supporters of this idea present.

Old men mate with young women as an explanation for long human lifespan

I meant to get into this PLoS One paper, but never got around to it. Here's a quick and dirty Yahoo! News story on it.

some data from the paper in the news story:

In all six groups, women stopped having children on average by their 50s, while some men continued to reproduce. The age after which men showed no reproduction varied among the groups and included:
Canada—Men showed fertility until 55 years old.
!Kung—55 years old
Gambia—75 years old
Yanomamo—70 years old
Ache—65 years old
Tsimane—60 years old

I think this complements the grandmother hypothesis as an explanation for long lifespans in humans. The take home message is that productivity in later age humans is highly valued due to a big productivity deficit in early life due to the importance of acquiring embodied capital due to our evolved feeding and social niche. (that was not well written, but hopefully kinda clear) - basically humans are altricial and require a lot of investment due to our ecological niche, therefore increasing payoffs to longevity and long-term productivity.... so that's why females prefer older guys who can provide such important child-rearing resources, since they have built up a lot of embodied capital, and also why older aged females can be vital (as grandparents).

Ethnic conflict, boundaries and cultural identity

I'm not too sure what to think of this paper. It's a really interesting topic, namely, the relative merits of maintaining cultural identity vs. cultural integration. I'm not a big fan of this kind of modeling, but the application of their model to geopolitical situations in the former Yugoslavia and India are interesting, although the Yugoslavia one is not very convincing. The figure shows A converted into their model B and then "Our prediction of populations likely to be in conflict with neighboring groups [red overlay, (C) and (D)] agrees well with the location of cities reported as sites of major fights and massacres [yellow dots, (D)]"
The implications that they draw in their conclusion are compelling though:

"It is worth considering whether, in places where cultural differentiation is taking place, conflict might be prevented or minimized by political acts that create appropriate boundaries suited to the current geocultural regions rather than the existing historically based state boundaries. Such boundaries need not inhibit trade and commerce and need not mark the boundaries of states, but should allow each cultural group to adopt independent behaviors in separate domains. Peaceful coexistence need not require complete integration."

Global Pattern Formation and Ethnic/Cultural Violence

May Lim, Richard Metzler, Yaneer Bar-Yam

Science 14 September 2007: Vol. 317. no. 5844, pp. 1540 - 1544

Abstract: We identify a process of global pattern formation that causes regions to differentiate by culture. Violence arises at boundaries between regions that are not sufficiently well defined. We model cultural differentiation as a separation of groups whose members prefer similar neighbors, with a characteristic group size at which violence occurs. Application of this model to the area of the former Yugoslavia and to India accurately predicts the locations of reported conflict. This model also points to imposed mixing or boundary clarification as mechanisms for promoting peace.

Personal genomics

The Genetic Genealogist has a post describing a new partnership between Illumina and a company called 23 and me. Basically any individual can send in their buccal cells and have their DNA typed for up to a million SNPs for about $600.
It looks as if Google may be getting in on this via one of the founder's wife who is the head of the company. There are many links to stories about this company at the Genetic Genealogist, including this one at Forbes.com.

"Initially, Flatley said, the company will be more focused on ancestry--questions like which parent one got more traits from, or who your distant relatives are--than medicine. Many researchers say most genetic discoveries are so far only of limited medical utility."

You can also check out the recent webcast detailing all this.

Slow-twitch version of ACTN-3 positively selected in Europeans and Asians

Razib has the abstract of a new paper in Nature Genetics about a study examining phenotypic effects in mice and signatures of selection around ACTN-3 in humans. One variant shows major differences between sub-Saharan Africans and others, and it has a pretty well documented role in muscle fiber composition (fast twitch vs. slow twitch) and the ability to be good at sprinting vs. endurance activity. see here, here, and here for related posts.

Social Brain Hypothesis

In this review (see abstract below), Dunbar and Shultz reviews some of the explanations for large brain size and discuss in greater detail the social brain hypothesis (SBH), suggesting that "balance of evidence now clearly favors the suggestion that it was the computational demands of living in large, complex societies that selected for large brains". They discuss some of the recent findings on the relationships between monogamy/enduring social bonds and large brain size.
Evolution in the Social Brain

R. I. M. Dunbar and Susanne Shultz

Science 7 September 2007: 1344-1347.

Abstract: The evolution of unusually large brains in some groups of animals, notably primates, has long been a puzzle. Although early explanations tended to emphasize the brain's role in sensory or technical competence (foraging skills, innovations, and way-finding), the balance of evidence now clearly favors the suggestion that it was the computational demands of living in large, complex societies that selected for large brains. However, recent analyses suggest that it may have been the particular demands of the more intense forms of pairbonding that was the critical factor that triggered this evolutionary development. This may explain why primate sociality seems to be so different from that found in most other birds and mammals: Primate sociality is based on bonded relationships of a kind that are found only in pairbonds in other taxa.

Starch and human evolution

Nature Genetics has a paper out on the differences in copy number of a gene (AMY1) that is involved in starch digestion between humans and other primates. The authors extend the implications of their findings a bit too far however (or at least they do in the BBC writeup) in saying that starch was more responsible than meat in allowing for a large brain.
The part on between-population differences in humans is pretty cool.
Check out some previous posts with a similar theme: USOs in hominin diet (USOs- underground storage organs, such as potatoes etc...) and the role of cooking in human evolution.

Diet and the evolution of human amylase gene copy number variation

George H Perry, Nathaniel J Dominy, Katrina G Claw, Arthur S Lee, Heike Fiegler, Richard Redon, John Werner, Fernando A Villanea, Joanna L Mountain, Rajeev Misra, Nigel P Carter, Charles Lee & Anne C Stone

Nature Genetics Published online: 9 September 2007

Abstract: Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch1, 2, 3. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis4. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number–variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Are highly conserved sequences what we think they are?

By the way, the elements they deleted are noncoding sequences, but likely play a role in gene regulation, but from Liza's Gross summary:

Mutations in genes near each of the other ultraconserved elements revealed a range of similarly lethal or severe abnormalities, ranging from neurological and sexual disorders to defective eye and kidney development. But in no case did the researchers find comparable aberrations in mice lacking the adjacent ultraconserved elements.

These results challenge the prevailing notion that highly conserved elements necessarily encode essential functions. Still, the researchers acknowledge that their experimental setup could have missed phenotypic changes that may have emerged under other conditions (in the wild, for example, or over multiple generations). Since all the ultraconserved elements were chosen based on their ability to promote transcription in lab tests—ensuring that the elements were capable of function—it's possible that deleting them produced no obvious effects because other elements stepped in to perform their job. Future studies can explore these possibilities and continue to probe the mechanisms that gave rise to such extreme evolutionary conservation. But for researchers relying on sequence constraint to shed light on the function of billions of noncoding base pairs in the human genome, the question remains: Why would evolution preserve these noncoding elements if their loss has no significant effect on the viability, fertility, and function of the organism?

Deletion of Ultraconserved Elements Yields Viable Mice

Nadav Ahituv, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A. Pennacchio, Edward M. Rubin

PLoS Biol 5(9): e234

Abstract: Ultraconserved elements have been suggested to retain extended perfect sequence identity between the human, mouse, and rat genomes due to essential functional properties. To investigate the necessities of these elements in vivo, we removed four noncoding ultraconserved elements (ranging in length from 222 to 731 base pairs) from the mouse genome. To maximize the likelihood of observing a phenotype, we chose to delete elements that function as enhancers in a mouse transgenic assay and that are near genes that exhibit marked phenotypes both when completely inactivated in the mouse and when their expression is altered due to other genomic modifications. Remarkably, all four resulting lines of mice lacking these ultraconserved elements were viable and fertile, and failed to reveal any critical abnormalities when assayed for a variety of phenotypes including growth, longevity, pathology, and metabolism. In addition, more targeted screens, informed by the abnormalities observed in mice in which genes in proximity to the investigated elements had been altered, also failed to reveal notable abnormalities. These results, while not inclusive of all the possible phenotypic impact of the deleted sequences, indicate that extreme sequence constraint does not necessarily reflect crucial functions required for viability.

Problems with Neandertal DNA sequence data

The implications are somewhat ambiguous, but it suggests that we should avoid any hasty conclusions from ancient DNA sequence.

Inconsistencies in Neanderthal genomic DNA sequences

Jeffrey D. Wall, Sung K. Kim

PLoS Genetics Early Online Release

Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.

East African "megadroughts" 100,000 years ago

via Anthropology.net, a new paper coming out in PNAS finds evidence of important climatic events that may, somehow(??), bear on important events in human evolution circa 100,000-50,000 years ago.

East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins

Christopher A. Scholz, Thomas C. Johnson, Andrew S. Cohen, John W. King, John A. Peck, Jonathan T. Overpeck, Michael R. Talbot, Erik T. Brown, Leonard Kalindekafe, Philip Y. O. Amoako, Robert P. Lyons, Timothy M. Shanahan, Isla S. Castañeda, Clifford W. Heil, Steven L. Forman, Lanny R. McHargue, Kristina R. Beuning, Jeanette Gomez, and James Pierson

Abstract: The environmental backdrop to the evolution and spread of early Homo sapiens in East Africa is known mainly from isolated outcrops and distant marine sediment cores. Here we present results from new scientific drill cores from Lake Malawi, the first long and continuous, high-fidelity records of tropical climate change from the continent itself. Our record shows periods of severe aridity between 135 and 75 thousand years (kyr) ago, when the lake's water volume was reduced by at least 95%. Surprisingly, these intervals of pronounced tropical African aridity in the early late-Pleistocene were much more severe than the Last Glacial Maximum (LGM), the period previously recognized as one of the most arid of the Quaternary. From these cores and from records from Lakes Tanganyika (East Africa) and Bosumtwi (West Africa), we document a major rise in water levels and a shift to more humid conditions over much of tropical Africa after 70 kyr ago. This transition to wetter, more stable conditions coincides with diminished orbital eccentricity, and a reduction in precession-dominated climatic extremes. The observed climate mode switch to decreased environmental variability is consistent with terrestrial and marine records from in and around tropical Africa, but our records provide evidence for dramatically wetter conditions after 70 kyr ago. Such climate change may have stimulated the expansion and migrations of early modern human populations.

Function, Phylogeny and Phenotype of MC1R in primates

They got MC1Rs from a bunch of different primates, put them into cells with an expression vector and tested for biochemical differences. I like how they specify their main questions at the end of the introduction:

"Is there variation in MC1R biochemical function among primates, and, if so, does this variation relate to primate phylogeny and/or coat color? Is the mechanism of red hair generation the same in orangutans and humans? Is there evidence for evolution of the relative importance of different control mechanisms on MC1R activity? Pharmacological characterization involved 2 types of assay: melanocortin ([Nle4, D-Phe7]-MSH and -MSH) -binding assays and second messenger (cAMP) assays in response to agonist (-MSH) and inhibitor/inverse agonist (ASIP)."

High Diversity in Functional Properties of Melanocortin 1 Receptor (MC1R) in Divergent Primate Species Is More Strongly Associated with Phylogeny than Coat Color

Tatjana Haitina, Aneta Ringholm, Joanne Kelly, Nicholas I. Mundy and Helgi B. Schiöth

Molecular Biology and Evolution 2007 24(9):2001-2008

Abstract: We have characterized the biochemical function of the melanocortin 1 receptor (MC1R), a critical regulator of melanin synthesis, from 9 phylogenetically diverse primate species with varying coat colors. There is substantial diversity in melanocyte-stimulating hormone (MSH) binding affinity and basal levels of activity in the cloned MC1Rs. MSH binding was lost independently in lemur and New World monkey lineages, whereas high basal levels of MC1R activity occur in lemurs and some New World monkeys and Old World monkeys. Highest levels of basal activity were found in the MC1R of ruffed lemurs, which have the E94K mutation that leads to constitutive activation in other species. In 3 species (2 lemurs and the howler monkey), we report the novel finding that binding and inhibition of MC1R by agouti signaling protein (ASIP) can occur when MSH binding has been lost, thus enabling continuing regulation of the melanin type via ASIP expression. Together, these findings can explain the previous paradox of a predominantly pheomelanic coat in the red ruffed lemur (Varecia rubra). The presence of a functional, MSH-responsive MC1R in orangutan demonstrates that the mechanism of red hair generation in this ape is different from the prevalent mechanism in European human populations. Overall, we have found unexpected diversity in MC1R function among primates and show that the evolution of the regulatory control of MC1R activity occurs by independent variation of 3 distinct mechanisms: basal MC1R activity, MSH binding and activation, and ASIP binding and inhibition. This diversity of function is broadly associated with primate phylogeny and does not have a simple relation to coat color phenotype within primate clades.

Overcoming HapMap ascertainment bias?

Check out Dienekes' post on a preprint AJHG paper. The authors discuss the acertainment bias in the markers chosen for HapMap and Perlegen. They resequenced "the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project." The major finding is that so-called common alleles differ in their "commonness" between groups - not very surprising. I guess the main take-home messages are the ascertainment bias in the HapMap SNPs and the consequent usefulness of their method, and a reaffirmation of the importance of "geographic ancestry", as they call it, when looking at the genetic basis for disease risk.

The structure of common genetic variation in U.S. populations

Stephen L. Guthery et al.

ABSTRACT: The common variant/common disease model predicts that most risk alleles underlying complex health-related traits are common and therefore old and found in multiple populations, rather than rare or population-specific. Accordingly, there is widespread interest in assessing the population structure of common alleles. However, such assessments have been confounded by analysis of datasets with bias toward ascertainment of common alleles (e.g., HapMap, Perlegen) or in which a relatively small number of genes and/or populations were sampled. The aim of this study was to examine the structure of common variation ascertained in major U.S. populations by resequencing the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project. The frequency distributions of private and common single nucleotide polymorphisms (SNPs) were measured, and the extent to which common SNPs were shared across populations was analyzed using several different estimators of population structure. Most SNPs that were common in one population were present in multiple populations, but SNPs common in one population were frequently not common in other populations. Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele.

Hybrid baboons and behavior

Behavioral variation and reproductive success of male baboons (Papio anubis x Papio hamadryas) in a hybrid social group.

Bergman TJ, Phillips-Conroy JE, Jolly CJ.

Am J Primatol. 2007 Aug 27; [Epub ahead of print]

Abstract: We take advantage of an array of hybrid baboons (Papio anubis x Papio hamadryas) living in the same social group to explore the causes and consequences of different male mating strategies. Male hamadryas hold one-male units and exhibit a sustained, intense interest in adult females, regardless of the latter's reproductive state. Anubis baboons, by contrast, live in multi-male, multi-female groups where males compete for females only when the latter are estrous. These two taxa interbreed to form a hybrid zone in the Awash National Park, Ethiopia, where previous work has suggested that hybrid males have intermediate and ineffective behavior. Here, we first examine male mating strategies with respect to morphological and genetic measures of ancestry. We found significant relationships between behavioral measures and morphology; males with more hamadryas-like morphology had more hamadryas-like behavior. However, genetic ancestry was not related to behavior, and in both cases intermediates displayed a previously unreported level of behavioral variation. Furthermore, male behavior was unrelated to natal group. Second, we evaluated reproductive success by microsatellite-based paternity testing. The highest reproductive success was found for individuals exhibiting intermediate behaviors. Moreover, over nine years, some genetically and morphologically intermediate males had high reproductive success. We conclude that the behavior of hybrid males is therefore unlikely to be an absolute barrier to admixture in the region.

SLC24A5 and population differentiation

Unfortunately, I don't have full text access to this one. SLC24A5 is a gene that was found to account for about 30% (I believe) of skin color variation between Africans and Europeans. It is also used as an AIM (ancestry informative marker) in admixture studies. Here are links to some other posts I have regarding the gene (here, here, here) and the paper in Science that originally described the locus in zebrafish and made the connection to humans.
In this paper, they find that using this locus in addition to Y-SNPs, it becomes feasible to differentiate some population groups.

The golden gene (SLC24A5) differentiates US sub-populations within the ethnically admixed Y-SNP haplogroups.

Sims LM, Ballantyne J.

Leg Med (Tokyo) 2007 Aug 24; [Epub ahead of print]

Abstract: Y-SNPs are currently being investigated for their potential to predict the ethnogeographic origin of the donor of a crime scene sample. Unfortunately, due to the presence of genetically admixed individuals within ethnic sub-populations within a particular haplogroup (hg), it is sometimes difficult to predict the ethnogeographic ancestry of an individual using only Y-SNPs. In the present work we determine the feasibility of using a combination of the golden pigmentation gene (SLC24A5) SNP and recently described high resolution Y-SNP markers to distinguish some of the different ethnic groups within particular Y-SNP hgs. Four hundred twenty-four individuals (128 African, 206 European, 50 Hispanic/Latin, 20 Pakistan, 20 E.Asian/Indian) were typed for a SNP within the golden gene. The Y-SNP hg was determined for all males and it was found that many of the European derived hg possessed a significant amount of ethnic admixture, with R1b3 having the most. We show the use of the golden gene, in combination with more informative Y-SNPs (U152, U106, and M222) and those that define the major hg, can differentiate between most of the African vs. European and African vs. E. Asian members of these heterogeneous populations.

Men /Women, Culture, and Group Selection

There's an article in the NYT entitled "Is There Anything Good About Men? And Other Tricky Questions" By John Tierney. It describes a recent speech by Roy Baumeister, a social psychologist. There's a few interesting excerpts from the article in addition to the somewhat obvious differences between men and women. Throughout it, Roy Baumeister invokes an assumption of group selection which I'm ok with to some extent, but which may rub people the wrong way especially with a phrase like "enabled the species to survive"!

“I’m certainly not denying that culture has exploited women,” he said. “But rather than seeing culture as patriarchy, which is to say a conspiracy by men to exploit women, I think it’s more accurate to understand culture (e.g., a country, a religion) as an abstract system that competes against rival systems — and that uses both men and women, often in different ways, to advance its cause.”

and then:

"Culture is not about men against women. By and large, cultural progress emerged from groups of men working with and against other men. While women concentrated on the close relationships that enabled the species to survive, men created the bigger networks of shallow relationships, less necessary for survival but eventually enabling culture to flourish. The gradual creation of wealth, knowledge, and power in the men’s sphere was the source of gender inequality. Men created the big social structures that comprise society, and men still are mainly responsible for this, even though we now see that women can perform perfectly well in these large systems.

What seems to have worked best for cultures is to play off the men against each other, competing for respect and other rewards that end up distributed very unequally. Men have to prove themselves by producing things the society values. They have to prevail over rivals and enemies in cultural competitions, which is probably why they aren’t as lovable as women."

Circumpolar populations and biology/health

I too think that there are many interesting research opportunities here. A few months ago AJHB had a special issue on circumpolar people and biology.

Arctic Peoples and Beyond: research opportunities in neuroscience and behaviour.

Duffy L, Bult-Ito A, Castillo M, Drew K, Harris M, Kuhn T, Ma Y, Schulte M, Taylor B, van Muelken M.

Int J Circumpolar Health. 2007 Jun;66(3):264-75.

OBJECTIVES: Arctic and northern peoples are spread across Alaska, Canada, Russia and the Scandinavian countries. Inhabiting a variety of ecosystems, these 4 million residents include Indigenous populations who total about 10% of the population. Although Arctic peoples have very diverse cultural and social systems, they have health issues related to environmental impacts and knowledge/treatment disparities that are common to other minority and Indigenous peoples around the world. Research that explores the neuroscience and behavioural aspects of these health disparities offers challenges and significant opportunities. As the next generation of neuroscientists enter the field, it is imperative that they view their contributions in terms of translational medicine to address health disparities. STUDY DESIGN: A workshop was designed to bring neuroscientists together to report on the current directions of neuroscience research and how it could impact health disparities in the North. This workshop produced research recommendations for the growth of neuroscience in the North. METHODS: On May 31, 2006 the National Institute of Neurological Disorders and Stroke, the Burroughs Wellcome Foundation, the Arctic Division of AAAS and the University of Alaska co-sponsored a workshop entitled "Arctic Peoples and Beyond: Decreasing Health Disparities through Basic and Clinical Research." Also, the role and goals of the International Union for Circumpolar Health (IUCH) were presented at the meeting. RESULTS: A set of recommendations related to research opportunities in neuroscience and behaviour research and ways to facilitate national and international partnerships were developed. CONCLUSIONS: These recommendations should help guide the development of future health research in circumpolar neuroscience and behaviour. They provide ideas about research support and informational exchange that will address health challenges.

For all you southpaws

I had to post on this one not only for its behavioral ecology significance, but also because I had my first start in science experimenting with fiddler crab circadian rhythms and pigmentation, back in high school. The advantage of having a left claw, they find, probably has to do with something other than a frequency dependent advantage in fighting ability. I like the straightforward question as posed in the title, although they should have included that they were asking the question in reference to fighting.
This is also interesting in the context of that recent paper on the left-handedness gene. Maybe they could check out that gene in the crab. In that paper they also went through an evolutionary explanation for left-handedness in humans.. sorry, don't have link to that paper. I think it was in Molecular Psychiatry.

What are the consequences of being left-clawed in a predominantly right-clawed fiddler crab?

P.R.Y. Backwell, M. Matsumasa, M. Double, A. Roberts, M. Murai, J.S. Keogh, M.D. Jennions

Proceedings Royal Society, B Online: Tuesday, August 21, 2007

Abstract: Male fiddler crabs (genus Uca) have an enlarged major claw that is used during fights. In most species, 50% of males have a major claw on the left and 50% on the right. In Uca vocans vomeris, however, less than 1.4% of males are left-clawed. Fights between opponents with claws on the same or opposite side result in different physical alignment of claws, which affects fighting tactics. Left-clawed males mainly fight opposite-clawed opponents, so we predicted that they would be better fighters due to their relatively greater experience in fighting opposite-clawed opponents. We found, however, that (i) a left-clawed male retains a burrow for a significantly shorter period than a size-matched right-clawed male, (ii) when experimentally displaced from their burrow, there is no difference in the tactics used by left- and right-clawed males to obtain a new burrow; however, right-clawed males are significantly more likely to initiate fights with resident males, and (iii) right-clawed residents engage in significantly more fights than left-clawed residents. It appears that left-clawed males are actually less likely to fight, and when they do fight they are less likely to win, than right-clawed males. The low-level persistence of left-clawed males is therefore unlikely to involve a frequency-dependent advantage associated with fighting experience.

Trivers-Willard tested

Trivers–Willard at birth and one year: evidence from US natality data 1983–2001

Douglas Almond, Lena Edlund

Proceedings of the Royal Society, B Volume 274, Number 1624 / October 07, 2007

Abstract: Trivers & Willard (TW) hypothesized that evolution would favour deviations from the population sex ratio in response to parental condition: parents in good condition would have more sons and parents in poor condition would have more daughters. We analyse the universe of US linked births and infant deaths to white mothers 1983–2001, covering 48 million births and 310000 deaths. We find that (i) married, better educated and younger mothers bore more sons and (ii) infant deaths were more male if the mother was unmarried and young. Our findings highlight the potential role of offspring sex ratio as an indicator of maternal status, and the role of infant mortality in shaping a TW pattern in the breeding population.

Sperm competition in chimps and humans

Functional evidence for differences in sperm competition in humans and chimpanzees

Matthew J. Anderson, Shannon J. Chapman, Elaine N. Videan, Erika Evans, Jo Fritz, Tara S. Stoinski, Alan F. Dixson, Pascal Gagneux

AJPA: published early online

Abstract: Sperm competition occurs when the gametes of or more males compete for opportunities to fertilize a given set of ova. Previous studies have demonstrated that certain morphological characteristics are affected by sperm competition intensity (e.g. relative testes size and sperm midpiece volume). This study examined whether aspects of sperm energetics may also be affected by sexual selection. We compared the membrane potential of mitochondria in live sperm between H. sapiens (single partner mating system) and P. troglodytes (multiple partner mating system). Flow cytometry of sperm stained with the carbocyanine fluorescent dye JC-1 (an assay for mitochondrial membrane potential) revealed marked differences in red fluorescence intensity. P. troglodytes sperm showed significantly higher mitochondrial membrane potential. Mitochondria provide a substantial part of the energy required for sperm motility. A higher mitochondrial loading may therefore be associated with enhanced sperm motility and/or longevity. Additionally, examination of JC-1 red fluorescence levels before and after in vitro capacitation revealed further differences. Whereas chimpanzee sperm showed maintenance of membrane potential after capacitation (in some cases even an increase), sperm from humans consistently showed reduction in membrane potential. These results indicate that the sperm of human beings and chimpanzees exhibit marked differences in mitochondrial function, which are affected by selection pressures relating to sperm competition and that these pressures differ significantly between humans and chimpanzees.

Americans are short and don't live very long

According to this news story in Discovery (via TAMU Anthro. in the News) Americans ranks 42nd in life expectancy. This follows a story a few months ago about Americans being short compared to other "Western" nations. (I assume they controlled for recent immigrants and other obvious confounders). From the Discovery story on life expectancy:

"A baby born in the United States in 2004 will live an average of 77.9 years. That life expectancy ranks 42nd, down from 11th two decades earlier, according to international numbers provided by the Census Bureau and domestic numbers from the National Center for Health Statistics.

Andorra, a tiny country in the Pyrenees mountains between France and Spain, had the longest life expectancy, at 83.5 years, according to the Census Bureau. It was followed by Japan, Macau, San Marino and Singapore."

The costs and benefits of being fat or skinny

on the trade-off between between being fat & slow & energetically buffered and lean & fast & prone to starvation. There could be several alternative explanations for their finding, but maybe they control for some of these.

Mass-dependent predation risk and lethal dolphin–porpoise interactions

R. MacLeod, C.D. MacLeod, J.A. Learmonth, P.D. Jepson, R.J. Reid, R. Deaville, G.J. Pierce

Proc. Roy. Soc. B Online: Tuesday, August 14, 2007

Abstract: In small birds, mass-dependent predation risk (MDPR) is known to make the trade-off between avoiding starvation and avoiding predation dependent on individual mass. This occurs because carrying increased fat reserves not only reduces starvation risk but also results in a higher predation risk due to reduced escape flight performance and/or the increased foraging exposure needed to maintain a higher body mass. In principle, the theory of MDPR could also apply to any animal capable of storing energy reserves to reduce starvation and whose escape performance decreases with increasing mass. We used a unique situation along certain parts of coastal Britain, where harbour porpoises (Phocoena phocoena) are pursued and killed but crucially not eaten by bottlenose dolphins (Tursiops truncatus), to investigate whether a MDPR effect can occur in non-avian species. We show that where high levels of dolphin ‘predation’ occur, porpoises carry significantly less energy reserves than would otherwise be expected and this equates to reducing by approximately 37% the length of time that a porpoise could survive without feeding. These results provide the first evidence that a mass-dependent starvation–predation risk trade-off may be a general ecological principle that can apply to widely different animal types rather than, as is currently thought, only to birds.

Spencer Wells on Colbert Report

I love the Colbert Report: (via Eye on DNA)

The genetics of pigmentation in beach mice

They looked at some mice in Florida, some of which have very light pigmentation, did crosses etc..., examined 11 candidate pigmentation genes (for mice) , did linkage and QTL analysis, and found a strong effect of MC1R and the agouti signaling protein. Most interestingly, they go into how they think the genes interact. (gene expression vs. coding region mutations, and epistasis)

some interesting parts from the conclusion:

Our results also have several implications for understanding the genetic basis of adaptation. First, this subspecific difference in color pattern is produced by a few interacting genes of large effect, supporting the idea that adaptations can involve relatively few genes rather than, as is often believed, many genes of small effect.

and,

These results support the idea that adaptation is not necessarily driven largely by cis-regulatory changes [29,30] or by (semi) dominant alleles. Third, we show that the nature of epistasis between Mc1r and Agouti in wild populations does not mirror that seen in the laboratory, suggesting that one should be cautious not only about extrapolating the genetics of laboratory strains to evolution in nature, but also about inferring the directionality of biochemical pathways from patterns of gene interactions. Finally, most genetic studies of morphological change have concentrated on the loss of phenotypic traits through loss-of-function mutations (e.g., reduced armor in stickleback fish [33,34], absence of wing spots in Drosophila [35], and lack of pigment in cavefish [36]). This study provides a novel example of how adaptation can result from mutations involving a gain of function.

Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes

Cynthia C. Steiner, Jesse N. Weber, Hopi E. Hoekstra

PLoS Biology early online Aug 14, 2007

Abstract: Little is known about the genetic basis of ecologically important morphological variation such as the diverse color patterns of mammals. Here we identify genetic changes contributing to an adaptive difference in color pattern between two subspecies of oldfield mice (Peromyscus polionotus). One mainland subspecies has a cryptic dark brown dorsal coat, while a younger beach-dwelling subspecies has a lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, we identified three chromosomal regions (two of major and one of minor effect) associated with differences in pigmentation traits. Two candidate genes, the melanocortin-1 receptor (Mc1r) and its antagonist, the Agouti signaling protein (Agouti), map to independent regions that together are responsible for most of the difference in pigmentation between subspecies. A derived mutation in the coding region of Mc1r, rather than change in its expression level, contributes to light pigmentation. Conversely, beach mice have a derived increase in Agouti mRNA expression but no changes in protein sequence. These two genes also interact epistatically: the phenotypic effects of Mc1r are visible only in genetic backgrounds containing the derived Agouti allele. These results demonstrate that cryptic coloration can be based largely on a few interacting genes of major effect.

Whites are a minority in 1 in 10 US counties

I wonder what Andrew at Statistical Modeling, Causal Inference, and Social Science would think about this figure. I think they could have done a much better job with it. It's just very hard to look at, especially because the county lines are too bold.

Lactase persistence allele - haplotype diversity

In this paper, the authors look at the 13910C/T allele that is pretty well known to be asociated with lactase persistence (LP) in Europeans and 8 markers in the 30 kb surrounding this particular allele among a set of global populations (1611 samples in 37 populations) - looking for patterns of diversity. They identified 9 haplotypes with the LP (13910-T) allele and 14 haplotypes with the non-LP allele. They were not able to reconcile the fact that the LP allele occured on two different haplotypic backgrounds, hence they assert that the mutation arose independently. Their age estimates of the mutation on the two different haplotypes also supposedly confirm this. I still don't quite get the gist and the methods in this paper. I'd probably have to read it a few more times.
Interestingly, the French have lactase persistence rate of only 58.8% while the neighboring Basques have a rate of 91.7%! ... and southern Italians only 11%! I wonder how much the environmental component of "getting used" to lactose over one's lifespan is that accounts for the ability to use/tolerate lactose... these percentages seem very low.

Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans

Nabil Sabri Enattah, Aimee Trudeau et al.

American Journal of Human Genetics Sept 2007

Abstract: A single-nucleotide variant, C/T-13910, located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T-13910 variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8–H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T-13910 H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T-13910 H98 allele (5,000–12,000 years old) is relatively older than the other geographically restricted LP alleles (1,400–3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T-13910 allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.

The role of CREs in evolution

first a description of CREs and their role from the paper, and then the abstract below:

"Most loci encoding pattern-regulating proteins were found to include multiple individual cis-regulatory elements (CREs), with each CRE typically comprising binding sites for multiple distinct transcription factors and controlling gene expression within a discrete spatial domain in a developing animal. The realization that the total expression pattern of a gene was the sum of many parts, each directed by distinct CREs, marked a profound change in concepts of gene regulation. The modular arrangement of CREs also had clear implications for evolutionary genetics, because it suggested a mechanism for how selective changes in gene expression and morphology could evolve in one part of the body, independent of other parts. The conservation of the biochemical activity of regulatory proteins, the divergence of their expression patterns across taxa, and the modular organization of CREs provided the basis for the general proposal that gene expression evolution, and therefore morphological evolution, would occur primarily through changes in cis-regulatory sequences controlling gene transcription."

Emerging principles of regulatory evolution

Benjamin Prud'homme, Nicolas Gompel, and Sean B. Carroll

PNAS | May 15, 2007 | vol. 104 | Suppl. 1 | 8605-8612

Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels.

Monogamy associated with larger brain

A paper entitled "The evolution of the social brain: Anthropoid primates contrast with other vertebrates" just came out in Proceedings of the Royal Society, B (a great journal, I would add). The article is open access, so the link will take you directly to the paper. The authors, Susanne Shultz and Robin Dunbar (of “social intelligence” or “social brain” hypothesis fame), examine the relationship between brain size and pairbonding/enduring social bonds. Previous research has attempted to correlate big brains with group size and amount of deception, for example. Basically the theory goes: Animals have large brains to deal with living in groups - it takes a big brain to be social.

The interesting thing that they find in this paper is that, in non-primate taxa, pairbonded species have larger brain sizes than would be predicted for group size. So there’s something about monogamy or related to monogamy that requires more brain power. In primates this effect does not happen. For them, those species that live in the largest groups have the larger brains. The authors give a short explanation as to why the pattern does not hold in primates, namely because in primates “these bonded relationships have been generalized to all social partners”. The authors also do a pretty good job of explaining many of the potential confounders (phylogeny, ecology etc…).

In the case of humans, it is hard to disentangle our ecological niche in terms of food type from our social systems. Some argue that we need large brains to obtain hard-to-get foods (meat, roots, nuts etc…) while others claim is that it’s our social complexity that requires a big brain. The two are not mutually exclusive since you need to be cooperative and have a social network to get food.

There’s got to be some way to separate these two, or some kind of comparative analysis that would separate the two variables (feeding ecology and sociality). And then, let’s not forget the sexual selection hypothesis that says that a large brain, in humans mainly, is the result of sexual selection.

The genetic affinities of click-speaking populations

Dienekes has the abstract to a paper called "History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation."

Genetics of human skin pigmentation

OCA2*481Thr , a hypofunctional allele in pigmentation, is characteristic of northeastern Asian populations

Journal of Human Genetics Volume 52, Number 8 / August, 2007

Isao Yuasa, Kazuo Umetsu, Shinji Harihara, Aya Miyoshi, Naruya Saitou, Kyung Sook Park, Bumbein Dashnyam, Feng Jin, Gérard Lucotte, Prasanta K. Chattopadhyay, Lotte Henke and Jürgen Henke

Abstract: Asians as well as Europeans have light skin, for which no genes to date are known to be responsible. A mutation, Ala481Thr (c.G1559A), in the oculocutaneous albinism type II (OCA2) gene has approximately 70% function of the wild type allele in melanogenesis. In this study, the distribution of the mutation was investigated in a total of 2,615 individuals in 20 populations from various areas. OCA2*481Thr prevailed almost exclusively in a northeastern part of Asia. The allele frequency was highest in Buryat (0.24) in Mongolia and showed a north–south downward geographical gradient. These findings suggest that OCA2*481Thr arose in a region of low ultraviolet radiation and thereafter spread to neighboring populations.

ACE in baboons and humans

genetic polymorphisms, phenotypes and cross species comparisons:

Parallel effects of genetic variation in ACE activity in baboons and humans

Jenny Tung, Johannes Rudolph, Jeanne Altmann, Susan C. Alberts

American Journal of Physical Anthropology 2007, Volume 134, Issue 1,1-8

Abstract: Like humans, savannah baboons (Papio sp.) show heritable interindividual variation in complex physiological phenotypes. One prominent example of such variation involves production of the homeostatic regulator protein angiotensin converting enzyme (ACE), which shows heritable variation in both baboons and humans. In humans, this phenotypic variation is associated with an Alu insertion-deletion polymorphism in the ACE gene, which explains approximately half of the variation in serum ACE activity. We identified a similar Alu insertion-deletion polymorphism in the baboon ACE homologue and measured its frequency in a wild population and a captive population of baboons. We also analyzed the contribution of ACE genotype at this indel to variation in serum ACE activity in the captive population. When conditioned on weight, a known factor affecting ACE activity in humans, age and ACE genotype both accounted for variance in ACE activity; in particular, we identified a significant nonadditive interaction between age and genotype. A model incorporating this interaction effect explained 21.6% of the variation in residual serum ACE activity. Individuals homozygous for the deletion mutation exhibited significantly higher levels of ACE activity than insertion-deletion heterozygotes at younger ages (10-14 years), but showed a trend towards lower levels of ACE activity compared with heterozygotes at older ages (15 years). These results demonstrate an interesting parallel between the genetic architecture underlying ACE variation in humans and baboons, suggesting that further attention should be paid in humans to the relationship between ACE genetic variation and aging.

Where did the Africans in Brazil come from?

I assume that in this paper they give some historical context to the bio-geographical origin of the African lineages found today among Black males in Africa.

The Phylogeography of African Brazilians.

Gonçalves VF, Carvalho CM, Bortolini MC, Bydlowski SP, Pena SD.

Hum Hered. 2008 Jul 25;65(1):23-32

Background/Aims: Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. Methods: We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. Results: Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. Conclusion: Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information.

The Grandfather hypothesis

I'm not sure what to think about this paper, nor do I have time to really think about it ... but I do have time to put pictures.

Selection for long lifespan in men: benefits of grandfathering?

M. Lahdenperä, A.F. Russell, V. Lummaa

Proc. Roy. Soc. B online before print

Abstract: Life-history theory suggests that individuals should live until their reproductive potential declines, and the lifespan of human men is consistent with this idea. However, because women can live long after menopause and this prolonged post-reproductive life can be explained, in part, by the fitness enhancing effects of grandmothering, an alternative hypothesis is that male lifespan is influenced by the potential to gain fitness through grandfathering. Here we investigate whether men, who could not gain fitness through reproduction after their wife's menopause (i.e. married only once), enhanced their fitness through grandfathering in historical Finns. Father presence was associated with reductions in offspring age at first reproduction and birth intervals, but generally not increases in reproductive tenure lengths. Father presence had little influence on offspring lifetime fecundity and no influence on offspring lifetime reproductive success. Overall, in contrast to our results for women in the same population, men do not gain extra fitness (i.e. more grandchildren) through grandfathering. Our results suggest that if evidence for a ‘grandfather’ hypothesis is lacking in a monogamous society, then its general importance in shaping male lifespan during our more promiscuous evolutionary past is likely to be negligible.

Variation, cont.

see smallest horse below largest horse:

Chimp vs. human punishment

This study is part of a recent line of research that examines how chimpanzees and humans are different. This one highlights the ultra-sociality of humans who are willing to undergo a net cost so that they can punish someone. ... like the ultimatum game, where an individual could accept an offer of 3 out of $10, but instead refuses to accept free money for the sake of fairness. There are several ways to interpret this. Humans are so extremely social, and punishment is a way of signalling that a person is more concerned about fairness and is willing to undergo a cost to show to others that he values fairness. In this way he gains a good reputation. It is hard to interpret behavior through these games, since it was not in a game-like environment that these behaviors evolved. Alternatively, this research could be used to argue that group selection is operating, since an individual is undergoing a net cost for the good of the group... although the counter-argument is that the individual is not undergoing a net cost - he is gaining a good reputation... bottom line here - humans are ultra-social.

Chimpanzees are vengeful but not spiteful

Keith Jensen, Josep Call, and Michael Tomasello

PNAS online before print July 20, 2007

Abstract: People are willing to punish others at a personal cost, and this apparently antisocial tendency can stabilize cooperation. What motivates humans to punish noncooperators is likely a combination of aversion to both unfair outcomes and unfair intentions. Here we report a pair of studies in which captive chimpanzees (Pan troglodytes) did not inflict costs on conspecifics by knocking food away if the outcome alone was personally disadvantageous but did retaliate against conspecifics who actually stole the food from them. Like humans, chimpanzees retaliate against personally harmful actions, but unlike humans, they are indifferent to simply personally disadvantageous outcomes and are therefore not spiteful.

Variation

It's all about the mutations

this one is probably worth a few reads...

The new mutation theory of phenotypic evolution

Masatoshi Nei

PNAS Published online before print

Abstract: Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

LD in African-Americans

making the case for the utility of admixed populations (with greater LD) in genotyping and association studies.

Dissecting Linkage Disequilibrium in African American Genomes: Roles of Markers and Individuals.

Xu S, Huang W, Wang H, He Y, Wang Y, Wang Y, Qian J, Xiong M, Jin L.

Mol Biol Evol. 2007 Jul 13; [Epub ahead of print]

Abstract: Substantial increases of linkage disequilibrium (LD) both in magnitude and in range have been observed in recently admixed populations such as African American (AfA). On the other hand, it has also been shown that LD in African Americans was very similar to that of African. In this study, we attempted to resolve these contradicting observations by conducting a systematic examination of the LD structure in African Americans by genotyping a sample of African American individuals at 24,341 SNPs spanning almost the entire chromosome 21, with an average density of 1.5 kb/SNP. The overall LD in African Americans is similar to that in African populations and much less than that in European populations. Even when the ancestry-informative markers (AIMs) were used, extended LD in AfA was found to be limited to certain magnitude range (0.2

Cranial sizes and distance from Africa

I wonder if their test is really able to detect if there was even a tiny bit of a "second origin"... otherwise this looks pretty cool, though haven't gone through the details.

The effect of ancient population bottlenecks on human phenotypic variation

Andrea Manica, William Amos, François Balloux & Tsunehiko Hanihara

Nature 448, 346-348 (19 July 2007)

Abstract: The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results, and have been argued to support multiple origins of modern humans. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19–25% of heritable variation in craniometric measurements—a remarkably strong effect for phenotypic measurements known to be under selection.

tables2graphs.com

Andrew at the "Statistical Modeling, Causal Inference, and Social Science" blog (that's a long name!) is often talking about how he think that graphs should always be used in favor of tables.
He has created a website called tables2graphs describing how this can be done and has developed some programs to do it.
I agree that tables are not as visually pleasing as graphs and I think that seeing data graphically can illuminate patterns that we might not otherwise see. The only advantage of tables that I can imagine is that with graphs you don't get the exact values, you just get eyeball guesses, but I'm sure they have some way of addressing that.

Lucy comes to Houston

Via TAMU Anthropology in the News, this is a story about how local Ethiopians are irate, for political and other reasons, at the arrival of Lucy to the Houston Museum, the first stop on her US tour. I had to post on this since I grew up in Houston and had some Ethiopian friends.
Ethiopians in Houston decry debut of Lucy fossil

Another paper on the evolution of human running

The evolution of human running: Effects of changes in lower-limb length on locomotor economy

Karen L. Steudel-Numbers, Timothy D. Weaver, and Cara M. Wall-Scheffler

Journal of Human Evolution Volume 53, Issue 2, August 2007, Pages 191-196

Abstract: Previous studies have differed in expectations about whether long limbs should increase or decrease the energetic cost of locomotion. It has recently been shown that relatively longer lower limbs (relative to body mass) reduce the energetic cost of human walking. Here we report on whether a relationship exists between limb length and cost of human running. Subjects whose measured lower-limb lengths were relatively long or short for their mass (as judged by deviations from predicted values based on a regression of lower-limb length on body mass) were selected. Eighteen human subjects rested in a seated position and ran on a treadmill at 2.68 m s−1 while their expired gases were collected and analyzed; stride length was determined from videotapes. We found significant negative relationships between relative lower-limb length and two measures of cost. The partial correlation between net cost of transport and lower-limb length controlling for body mass was r = −0.69 (p = 0.002). The partial correlation between the gross cost of locomotion at 2.68 m s−1 and lower-limb length controlling for body mass was r = −0.61 (p = 0.009). Thus, subjects with relatively longer lower limbs tend to have lower locomotor costs than those with relatively shorter lower limbs, similar to the results found for human walking. Contrary to general expectation, a linear relationship between stride length and lower-limb length was not found.

Sexually antagonistic traits maintain genetic variation in populations

This paper looks really interesting. I don't know if I buy it, and don't have time to make that determination now. The maintenance of high levels of genetic variation in populations is a fascinating topic.

Sexually antagonistic genetic variation for fitness in red deer

Katharina Foerster, Tim Coulson, Ben C. Sheldon, Josephine M. Pemberton, Tim H. Clutton-Brock & Loeske E. B. Kruuk

Nature 447, 1107-1110 (28 June 2007) |

Abstract: Evolutionary theory predicts the depletion of genetic variation in natural populations as a result of the effects of selection, but genetic variation is nevertheless abundant for many traits that are under directional or stabilizing selection. Evolutionary geneticists commonly try to explain this paradox with mechanisms that lead to a balance between mutation and selection. However, theoretical predictions of equilibrium genetic variance under mutation–selection balance are usually lower than the observed values, and the reason for this is unknown. The potential role of sexually antagonistic selection in maintaining genetic variation has received little attention in this debate, surprisingly given its potential ubiquity in dioecious organisms. At fitness-related loci, a given genotype may be selected in opposite directions in the two sexes. Such sexually antagonistic selection will reduce the otherwise-expected positive genetic correlation between male and female fitness. Both theory and experimental data suggest that males and females of the same species may have divergent genetic optima, but supporting data from wild populations are still scarce. Here we present evidence for sexually antagonistic fitness variation in a natural population, using data from a long-term study of red deer (Cervus elaphus). We show that male red deer with relatively high fitness fathered, on average, daughters with relatively low fitness. This was due to a negative genetic correlation between estimates of fitness in males and females. In particular, we show that selection favours males that carry low breeding values for female fitness. Our results demonstrate that sexually antagonistic selection can lead to a trade-off between the optimal genotypes for males and females; this mechanism will have profound effects on the operation of selection and the maintenance of genetic variation in natural populations.