Inbreeding and the Spanish Hapsburgs

Since, presumably, the remains of these royals have been preserved, it would be interesting at some future date to carry out an ancient DNA study which would show exactly which deleterious alleles contributed to the morbidity of the Spanish Hapsburgs.

PLoS ONE doi:10.1371/journal.pone.0005174

The Role of Inbreeding in the Extinction of a European Royal Dynasty

Gonzalo Alvarez et al.

Abstract

The kings of the Spanish Habsburg dynasty (1516–1700) frequently married close relatives in such a way that uncle-niece, first cousins and other consanguineous unions were prevalent in that dynasty. In the historical literature, it has been suggested that inbreeding was a major cause responsible for the extinction of the dynasty when the king Charles II, physically and mentally disabled, died in 1700 and no children were born from his two marriages, but this hypothesis has not been examined from a genetic perspective. In this article, this hypothesis is checked by computing the inbreeding coefficient (F) of the Spanish Habsburg kings from an extended pedigree up to 16 generations in depth and involving more than 3,000 individuals. The inbreeding coefficient of the Spanish Habsburg kings increased strongly along generations from 0.025 for king Philip I, the founder of the dynasty, to 0.254 for Charles II and several members of the dynasty had inbreeding coefficients higher than 0.20. In addition to inbreeding due to unions between close relatives, ancestral inbreeding from multiple remote ancestors makes a substantial contribution to the inbreeding coefficient of most kings. A statistically significant inbreeding depression for survival to 10 years is detected in the progenies of the Spanish Habsburg kings. The results indicate that inbreeding at the level of first cousin (F = 0.0625) exerted an adverse effect on survival of 17.8%±12.3. It is speculated that the simultaneous occurrence in Charles II (F = 0.254) of two different genetic disorders: combined pituitary hormone deficiency and distal renal tubular acidosis, determined by recessive alleles at two unlinked loci, could explain most of the complex clinical profile of this king, including his impotence/infertility which in last instance led to the extinction of the dynasty.

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Facebook-using college students get lower grades

The question is: is Facebook responsible for distracting students from studying, or do students who would rather not study anyway spend more time on Facebbok? I am inclined to favor the latter explanation.

Facebook Use Linked To Lower Grades In College

College students who use Facebook spend less time studying and have lower grade point averages than students who have not signed up for the social networking website, according to a pilot study at one university.

However, more than three-quarters of Facebook users claimed that their use of the social networking site didn’t interfere with their studies.

“We can’t say that use of Facebook leads to lower grades and less studying – but we did find a relationship there,” said Aryn Karpinski, co-author of the study and a doctoral student in education at Ohio State University.

“There’s a disconnect between students’ claim that Facebook use doesn’t impact their studies, and our finding showing they had lower grades and spent less time studying.”

...

The researchers surveyed 219 students at Ohio State, including 102 undergraduate students and 117 graduate students. Of the participants, 148 said they had a Facebook account.

...

“It may be that if it wasn’t for Facebook, some students would still find other ways to avoid studying, and would still get lower grades. But perhaps the lower GPAs could actually be because students are spending too much time socializing online.”

Origin of African Pygmies

From the paper:

Finally, our estimates of gene flow between each group of Pygmies and agricultural populations yielded contrasting values, with levels of gene flow between WPYG and AGR populations three to seven times higher than those between EPYG and AGR populations (Table 2). This result, together with those obtained with protein markers [27], mtDNA [8],[36] and autosomal microsatellites [41],[46], indicates that (i) substantial gene flow has occurred between Western Pygmies and agricultural populations, possibly during a period before the strong social barriers currently separating these two groups became established [29],[32],[33],[41],[56], and (ii) the Eastern Mbuti Pygmies (i.e., the EPYG group in the filtered population dataset) have probably been among the most isolated Pygmy populations of sub-Saharan Africa.

Related:

• Maternal common ancestry between pygmies and farmers in Central Africa
• Common origin and differential admixture in Western Central African pygmies

Here are some pictures of Mbuti Pygmies from a National Geographic article.

PLoS Genetics doi:Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

Etienne Patin et al.

Abstract

The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter–gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter–gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events—size changes, population splits, and gene flow—ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter–gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of ~33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter–gatherers and farming populations ~60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups ~20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.

Link

Synonymous mutations not evolutionarily neutral

Synonymous mutations are changes in the DNA sequence that do not affect the type of amino acids produced. For this reason they have been thought of as neutral in terms of evolution and thus unaffected by selection (although see here for criticisms of tests using the synonymous/non-synonymous ratio to detect selection).

The new paper in Science shows how synonymous mutations affect gene expression, and thus phenotypes. From ScienceDaily:

Synonymous mutations do not change the amino-acid sequence of a protein, but they can nevertheless influence the amount of the protein that is produced. The researchers identified the mechanism underlying this regulation: synonymous mutations determine mRNA folding and thereby the eventual protein level. The researchers also identified a class of mutations that did not directly affect protein levels but slowed bacterial growth.

For biologists, these results fundamentally change the understanding of the role of synonymous mutations, which were previously considered evolutionarily neutral.

Science doi:10.1126/science.1170160

Coding-Sequence Determinants of Gene Expression in Escherichia coli

Grzegorz Kudla et al.

Abstract

Synonymous mutations do not alter encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.

Link

Strong apes and fast humans

The paper is freely accessible.

Current Anthropology doi:10.1086/592023

The Strength of Great Apes and the Speed of Humans

Alan Walker

Abstract

Cliff Jolly developed a causal model of human origins in his paper “The Seed‐Eaters,” published in 1970. He was one of the first to attempt this, and the paper has since become a classic. I do not have such grand goals; instead, I seek to understand a major difference between the living great apes and humans. More than 50 years ago, Maynard Smith and Savage (1956) showed that the musculoskeletal systems of mammals can be adapted for strength at one extreme and speed at the other but not both. Great apes are adapted for strength—chimpanzees have been shown to be about four times as strong as fit young humans when normalized for body size. The corresponding speed that human limb systems gain at the expense of power is critical for effective human activities such as running, throwing, and manipulation, including tool making. The fossil record can shed light on when the change from power to speed occurred. I outline a hypothesis that suggests that the difference in muscular performance between the two species is caused by chimpanzees having many fewer small motor units than humans, which leads them, in turn, to contract more muscle fibers earlier in any particular task. I outline a histological test of this hypothesis.

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Parental investment on adopted children

I can think of at least three reasons for the more negative outcomes of adopted children: (i) negative early pre-adoption experiences, (ii) relatively negative genetic background of children put up for adoption compared to the general population, or (iii) genetic discordance between parents and adopted children that make their relationship more difficult.

Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2009.01.001

Differential parental investment in families with both adopted and genetic children

Kyle Gibson

Abstract

Stepchildren are abused, neglected and murdered at higher rates than those who live with two genetically related parents. Daly and Wilson used kin selection theory to explain this finding and labeled the phenomenon “discriminative parental solicitude.” I examined discriminative parental solicitude in American households composed of both genetic and unrelated adopted children. In these families, kin selection predicts parents should favor their genetic children over adoptees. Rather than looking at cases of abuse, neglect, homicide and other antisocial behavior, I focused on the positive investments parents made in their children as well as the outcomes of each child. The results show that parents invested more in adopted children than in genetically related ones, especially in educational and personal areas. At the same time, adoptees experienced more negative outcomes. They were more likely to have been arrested, to have been on public assistance and to require treatment for drug, alcohol or mental health issues. They also completed fewer years of schooling and were more likely to divorce. In adoptive families, it appears that “the squeaky wheel gets the grease.” Parents invest more in adoptees not because they favor them, but because they are more likely than genetic children to need the help. I conclude that discriminative parental solicitude differs in adoptive and step households because adoptive families generally result from prolonged parenting effort, not mating effort like stepfamilies.

Link

Reading, Intelligence and Memory in Children

Behav Genet. 2009 Apr 4.

Genetic Covariance Structure of Reading, Intelligence and Memory in Children

van Leeuwen M, van den Berg SM, Peper JS, Hulshoff Pol HE, Boomsma DI.

This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained by a common genetic factor for reading performance, IQ, WM and STM and a genetic factor that only influenced reading performance and verbal memory. Genetic variation explained 83% of the variation in reading performance; most of this genetic variance was explained by variation in IQ and memory performance. We hypothesize, based on these results, that children with reading problems possibly can be divided into three groups: (1) children low in IQ and with reading problems; (2) children with average IQ but a STM deficit and with reading problems; (3) children with low IQ and STM deficits; this group may experience more reading problems than the other two.

Link

Arabian Genealogy

This is not a topic that is much known or discussed outside the Arab world, but it's certainly a very interesting one due to the patrilineal descent observed by traditional Arabian tribes.

Getting to the roots of family trees

According to Mr al Matroushi, Arabic family trees were kept diligently during the pre-Islamic period, between the time of Jesus and the Prophet Mohammed; with the expansion of Islamic influence beyond the Arabian peninsula, however, there was a lot of mixing and it became increasingly difficult to keep track of the various branches of far-flung families.

However, he says all Arab tribes can trace their origins to two main ones, the Qahtaniya and Adnaniya, that are direct descendants of Ismail, son of the Prophet Ibrahim. Prophet Mohammed’s ancestry is from the Adnaniya tribe.

...

Mr al Shehhi has published a book about the outcome of DNA testing on some of the main tribes in the UAE; he concluded that all the Emirati tribes come from “three fathers”, tens of thousands of years ago.

The UAE tribes, he says, “are the same as the rest of the Arabian tribes as there was no UAE or Saudi Arabia or any specific country; it was all open land and the tribes moved around.”

In genetics, the various major branches of the family tree of the human race are defined as “haplogroups”. According to genetic theory, says Mr Shehhi, the entire human race came from one man and one woman, labelled as “Adam” and “Eve”, and both came from Africa.

The samples taken by Mr al Shehhi from UAE tribes show about 70 per cent of them are from haplogroup J1 and the rest are from J2 and E1B1. The “father”, labelled by genetic science as J1, came from an area we know now as Iraq; J2 came from the area north of modern-day Syria and E1B1 from Syria itself.

mtDNA haplogroup U2d and medieval nomads

Hum Biol. 2008 Oct;80(5):565-71.

Mitochondrial haplogroup u2d phylogeny and distribution.

Malyarchuk B, Derenko M, Perkova M, Vanecek T.

Abstract

The sequencing of the entire mitochondrial DNA belonging to haplogroup U2d reveals that this clade is defined by four coding-region mutations at positions 1700, 4025, 11893, and 14926. Phylogenetic analysis suggests that western Eurasian haplogroup U2d appears to be a sister clade with the Indo-Pakistani haplogroup U2c. Results of a phylogeographic analysis of published population data on the distribution of haplogroup U2d indicate that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from the Caucasus and eastern Europe to central Europe.

Link

Mitochondrial DNA Haplogroups and Lipoatrophy After Antiretroviral Therapy.

J Acquir Immune Defic Syndr

Mitochondrial DNA Haplogroups Influence Lipoatrophy After Highly Active Antiretroviral Therapy.

Hendrickson SL, Kingsley LA, Ruiz-Pesini E, Poole JC, Jacobson LP, Palella FJ, Bream JH, Wallace DC, Oʼbrien SJ

Abstract

Although highly active antiretroviral therapy (HAART) has been extremely effective in lowering AIDS incidence among patients infected with HIV, certain drugs included in HAART can cause serious mitochondrial toxicities. One of the most frequent adverse events is lipoatrophy, which is the loss of subcutaneous fat in the face, arms, buttocks, and/or legs as an adverse reaction to nucleoside reverse transcriptase inhibitors. The clinical symptoms of lipoatrophy resemble those of inherited mitochondrial diseases, which suggest that host mitochondrial genotype may play a role in susceptibility. We analyzed the association between mitochondrial haplogroup and severity of lipoatrophy in HIV-infected European American patients on HAART in the Multicenter AIDS cohort Study and found that mitochondrial haplogroup H was strongly associated with increased atrophy [arms: P = 0.007, odds ratio (OR) = 1.77, 95% confidence interval (CI) = 1.17 to 2.69; legs: P = 0.037, OR = 1.54, 95% CI = 1.03 to 2.31; and buttocks: P = 0.10, OR = 1.41 95% CI = 0.94 to 2.12]. We also saw borderline significance for haplogroup T as protective against lipoatrophy (P = 0.05, OR = 0.52, 95% CI = 0.20 to 1.00). These data suggest that mitochondrial DNA haplogroup may influence the propensity for lipoatrophy in patients receiving nucleoside reverse transcriptase inhibitors.

Link

European School Survey on Alcohol and Other Drugs

The ESPAD 2007 report (pdf) has been released, and has received coverage from various countries (e.g., UK UK Ireland Malta Slovenia Czech Republic). Here is a summary of the results for Greece. The lower than average cigarette consumption, coupled with an apparently decreasing trend may be a hopeful sign for younger generations of Greeks.

Greece is one of the countries that reported rather moderate alcohol, tobacco and other drug habits.
However, the proportion of students who had been drinking alcohol during the past 12 months (87%) is somewhat higher than the ESPAD average. Being drunk, on the other hand, is not as common in Greece as in many other ESPAD countries: one fourth (26%) of the students reported this. Estimated consumption on the latest drinking day (3.1 cl alc. 100%) was also lower than average. About one-fifth (22%) of the Greek participants had been smoking during the past 30 days, which is lower than average. The lifetime prevalence of cannabis use (6%) is also low, at about one third of the ESPAD mean. Use of drugs other than cannabis (5%), on the other hand, is close to average. Rather small proportions of students report other behaviours such as lifetime use of inhalants (9%), non-prescription use of tranquillisers or sedatives (4%) and combined use of alcohol and pills (3%).

Internal variation within mtDNA macro-haplogroup R0

PLoS ONE doi:10.1371/journal.pone.0005112

New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0

Vanesa Álvarez-Iglesias et al.

Abstract

Background

R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (~40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.

Methodology/Principal Findings

We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (~57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6±8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).

Conclusions/Significance

In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.

Link

Humans at tropical latitudes produce more baby girls

Royal Society: Biology Letters doi:10.1098/rsbl.2009.0069

Humans at tropical latitudes produce more females

Kristen J. Navara

Abstract

Skews in the human sex ratio at birth have captivated scientists for over a century. The accepted average human natal sex ratio is slightly male biased, at 106 males per 100 females or 51.5 per cent males. Studies conducted on a localized scale show that sex ratios deviate from this average in response to a staggering number of social, economical and physiological variables. However, these patterns often prove inconsistent when expanded to other human populations, perhaps because the nature of the influences themselves exhibit substantial cultural variation. Here, data collected from 202 countries over a decade show that latitude is a primary factor influencing the ratio of males and females produced at birth; countries at tropical latitudes produced significantly fewer boys (51.1% males) annually than those at temperate and subarctic latitudes (51.3%). This pattern remained strong despite enormous continental variation in lifestyle and socio-economic status, suggesting that latitudinal variables may act as overarching cues on which sex ratio variation in humans is based.

Link

Ancient mtDNA from La Palma (Canary Islands)

Related posts:

• Origin of Canary Islanders
• mtDNA from 17th-18th c. Tenerife

European Journal of Human Genetics doi:10.1038/ejhg.2009.46

The maternal aborigine colonization of La Palma (Canary Islands)

Rosa Fregel et al.

Abstract

Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.2 +/- 2.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.4+/-2.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.

Link

Origin of the Meroites

Wikipedia entry on Meroe.

International Journal of Osteoarchaeology doi:10.1002/oa.1055

Who were the Meroites? A biological investigation into the Nubian post-hiatus group

K Godde

Abstract

Scholars have identified a hiatus in the archaeological record of Lower Nubia that spans approximately 1000 years. This interval may represent a desertion of Lower Nubia by its inhabitants. Evidence of occupation did not reappear in the area until the Meroitic time period. However, the identity of the returning people has been the subject of speculation. In order to determine who the Meroites of Lower Nubia were, 20 cranial non-metric traits were observed on six Nubian groups, representing five time periods. Two groups date to time periods immediately before (Kerma) and immediately after (X-Group) the Meroitic period. Three additional Nubian groups (two Christian samples from different sites and Sesebi, a contemporary sample) were utilised as outgroups to elucidate a clearer picture of the relationship among the six samples. Mahalanobis D² with a tetrachoric matrix was employed for calculating biological distances among the groups. Principal coordinates analysis produced two clusters of Nubians, where the Meroitics clustered with other Nubian groups. Specific distance scores indicate the Meroites were biologically similar to individuals from the time periods prior to and after their arrival in Lower Nubia. The Meroites therefore appear to be a Nubian group returning to Lower Nubia after its desertion.

Link

Nei critical of tests for detecting selection in humans

The paper isn't online yet (post will be updated when it is) so it's not clear which studies come under criticism. From the press release, it seems that there are at least two problems detected: tests using ratios of synonymous/nonsynonymous mutations, and small sample size numbers. As always, I am very fond of this type of whistle-blowing paper that examines a widely, but uncritically used technique which has formed the basis of numerous recent studies.

Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

PNAS doi:10.1073/pnas.0901855106

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

Masafumi Nozawa et al.

Abstract

Natural selection operating in protein-coding genes is often studied by examining the ratio (ω) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is ≈80 or smaller. Because the ω value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high ω values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high ω value. To understand adaptive evolution, some form of experimental confirmation is necessary.


Link